TeSS Training eSupport System

Week 1: Using R / Bioconductor in AnVIL

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workshop

Week 1: Using R / Bioconductor in AnVIL https://bioconductor.orghttps://docs.google.com/document/d/18aNzWpt55I-dni9l0IZTB2G3oDOU4X07PyKGXFGyb40/edit https://tess.elixir-europe.org/materials/week-1-using-r-bioconductor-in-anvil Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Workshop

Lecture 19: Gene Set Enrichment Analysis

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: GSEA

Lecture 19: Gene Set Enrichment Analysis https://bioconductor.org/help/course-materials/2019/CSAMA/lecture-19-gene-set-enrichment.pdf https://tess.elixir-europe.org/materials/lecture-19-gene-set-enrichment-analysis Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan GSEA

Testing R Packages

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Testing R Packages https://bioconductor.org2021/BiocDevelForum/19-testing.pdf https://tess.elixir-europe.org/materials/testing-r-packages Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Dirk Eddelbuettel

R and Bioconductor for Genomic Analysis

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intro

R and Bioconductor for Genomic Analysis https://bioconductor.org2017/OSU/A1_Using_R.html https://tess.elixir-europe.org/materials/r-and-bioconductor-for-genomic-analysis Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Intro

Methylation and regulatory work flows with minfi

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Methylation and regulatory work flows with minfi https://bioconductor.org2015/SeattleApr2015/G_Methylation.html https://tess.elixir-europe.org/materials/methylation-and-regulatory-work-flows-with-minfi Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Performance and parallel evaluation

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Performance

Performance and parallel evaluation https://bioconductor.org2016/CSAMA/lect-19-big-data/lect-19-big-data.pdf https://tess.elixir-europe.org/materials/performance-and-parallel-evaluation Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Performance

Working with Genomic Ranges

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Genomics

Working with Genomic Ranges https://bioconductor.org2014/SeattleFeb2014/Ranges.pdf https://tess.elixir-europe.org/materials/working-with-genomic-ranges Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Genomics

Experimental design

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Experimental design

Experimental design https://bioconductor.org2016/CSAMA/lect-09-expdesign/ExperimentalDesign.pdf https://tess.elixir-europe.org/materials/experimental-design Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Charlotte Soneson Experimental design

Challenges and opportunities

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Challenges and opportunities https://bioconductor.org2020/HCASymposium/06-ChallengesAndOpportunities.pdf https://tess.elixir-europe.org/materials/challenges-and-opportunities Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Kasper Hansen

Working with R

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: R/Bioconductor

Working with R https://bioconductor.org2014/SeattleFeb2014/R_slides.pdf https://tess.elixir-europe.org/materials/working-with-r Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan R/Bioconductor

Single cell updates

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Single cell updates https://bioconductor.org/help/course-materials/2019/BiocDevelForum/01-SingleCell.pptx https://tess.elixir-europe.org/materials/single-cell-updates Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Aaron Lun

Lecture: HiC data analysis

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: HiC

Lecture: HiC data analysis https://bioconductor.org2015/CSAMA2015/lect/L13-hi-c-pekowska.pdf https://tess.elixir-europe.org/materials/lecture-hic-data-analysis Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Aleksandra Pȩkowska HiC

Workshops

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Conference

Workshops https://bioconductor.orghttps://rebrand.ly/biocworkshops2019 https://tess.elixir-europe.org/materials/workshops Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Various Conference

R / Bioconductor for open-source analysis and comprehension of high-throughput genomic data

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

R / Bioconductor for open-source analysis and comprehension of high-throughput genomic data https://bioconductor.orghttps://docs.google.com/presentation/d/e/2PACX-1vS25aIVGDGCAJMsG1VNIxKaUbU7tsefGwMzAIxBLtUJG8ZO44m0zjYRvajli18xSbzwCgFrU_Zlb9kq/pub?start=false&loop=false&delayms=3000 https://tess.elixir-europe.org/materials/r-bioconductor-for-open-source-analysis-and-comprehension-of-high-throughput-genomic-data Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Orchestrating single cell analysis with Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Orchestrating single cell analysis with Bioconductor https://bioconductor.orghttps://docs.google.com/presentation/d/1pQZJUfsj4rQ38N28PeDFHJ1ocnuzcamFKCgxfAEO51s/edit#slide=id.p https://tess.elixir-europe.org/materials/orchestrating-single-cell-analysis-with-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Stephanie Hicks

Presentation on AnVIL

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Presentation on AnVIL https://bioconductor.org2020/BiocDevelForum/14-AnVIL.mp4 https://tess.elixir-europe.org/materials/presentation-on-anvil Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Day 1 European Bioconductor Meeting 2017

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Conference

Day 1 European Bioconductor Meeting 2017 https://bioconductor.orghttps://www.youtube.com/watch?v=d3PPpAapDVc&list=LLqaMSQd_h-2EDGsU6WDiX0Q https://tess.elixir-europe.org/materials/day-1-european-bioconductor-meeting-2017 Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Various authors Conference

Evening session: Efficient R

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Big data

Evening session: Efficient R https://bioconductor.org/help/course-materials/2019/CSAMA/efficient_r.html https://tess.elixir-europe.org/materials/evening-session-efficient-r Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Big data

Discussion about unit testing

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Discussion about unit testing https://bioconductor.org2020/BiocDevelForum/09-testing.mp4 https://tess.elixir-europe.org/materials/discussion-about-unit-testing Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Various

Developing robust and efficient code

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workshop

Developing robust and efficient code https://bioconductor.org/help/course-materials/2019/NURDS/NURDS.html https://tess.elixir-europe.org/materials/developing-robust-and-efficient-code Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Workshop

New builder update

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

New builder update https://bioconductor.org2020/BiocDevelForum/13-DevelForum01.mp4 https://tess.elixir-europe.org/materials/new-builder-update Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Hervé Pagès

Presentation on sparseMatrixStats

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Presentation on sparseMatrixStats https://bioconductor.org2020/BiocDevelForum/15-sparseMatrixStats.pdf https://tess.elixir-europe.org/materials/presentation-on-sparsematrixstats Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Constantin Ahlmann-Eltze

Browsing and searching the Bioconductor codebase

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Browsing and searching the Bioconductor codebase https://bioconductor.org2020/BiocDevelForum/13-BiocCodeTools.pdf https://tess.elixir-europe.org/materials/browsing-and-searching-the-bioconductor-codebase Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Mike Smith

RNA-Seq Lab: Workflow -- gene-level exploratory analysis and differential expression

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

RNA-Seq Lab: Workflow -- gene-level exploratory analysis and differential expression https://bioconductor.org/help/workflows/rnaseqGene/ https://tess.elixir-europe.org/materials/rna-seq-lab-workflow-gene-level-exploratory-analysis-and-differential-expression Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Michael Love et al. RNA-Seq

Compiling the OSCA book on the Bioconductor build system

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Compiling the OSCA book on the Bioconductor build system https://bioconductor.org2020/BiocDevelForum/13-DevelForum02.mp4 https://tess.elixir-europe.org/materials/compiling-the-osca-book-on-the-bioconductor-build-system Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Aaron Lun

Lecture 1: Introduction to R and Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: introduction

Lecture 1: Introduction to R and Bioconductor https://bioconductor.org/help/course-materials/2019/CSAMA/lecture-01-r-intro.html https://tess.elixir-europe.org/materials/lecture-1-introduction-to-r-and-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan introduction

Working with Ranges infrastructure: annotating and understanding regions

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Working with Ranges infrastructure: annotating and understanding regions https://bioconductor.org2014/CSAMA2014/4_Thursday/labs/Annotation_lab.pdf https://tess.elixir-europe.org/materials/working-with-ranges-infrastructure-annotating-and-understanding-regions Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

How to advance science using Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

How to advance science using Bioconductor https://bioconductor.orghttps://docs.google.com/presentation/d/e/2PACX-1vRf4SGj0Bfi-0i2Ni94EdSqghivfOWqEOvaI2eYCXNEdmr4dMEFhZnnHKVn9kzWwfg1ECcX9xpvsZ9y/pub https://tess.elixir-europe.org/materials/how-to-advance-science-using-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Machine Learning

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Machine learning

Machine Learning https://bioconductor.org2014/SeattleOct2014/B02.3_MachineLearning.html https://tess.elixir-europe.org/materials/machine-learning Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Sonali Arora Machine learning

Work in Progress: Bioconductor and the HCA

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Work in Progress: Bioconductor and the HCA https://bioconductor.orghttps://docs.google.com/presentation/d/1bKVCw8ByDG8UTQpE0pBMZ9RFqu0dP9AXNskynpxtdG0/edit#slide=id.p https://tess.elixir-europe.org/materials/work-in-progress-bioconductor-and-the-hca Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Introduction to DataFrames and the impact of recent changes

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Introduction to DataFrames and the impact of recent changes https://bioconductor.org/help/course-materials/2019/BiocDevelForum/02-DataFrame.pdf https://tess.elixir-europe.org/materials/introduction-to-dataframes-and-the-impact-of-recent-changes Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Hervé Pagès

01: Introduction to R and Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intro

01: Introduction to R and Bioconductor https://bioconductor.org/help/course-materials/2019/BSS2019/01_IntroToRAndBioconductor.html https://tess.elixir-europe.org/materials/01-introduction-to-r-and-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Intro

Gene set enrichment - Introduction

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Gene set enrichment - Introduction https://bioconductor.org2016/CSAMA/lect-17-gene-set-enrichment/lect-17-gene-set-enrichment.pdf https://tess.elixir-europe.org/materials/gene-set-enrichment-introduction Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

BioC 2018: Where Software and Biology Connect

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Conference

BioC 2018: Where Software and Biology Connect https://bioconductor.orghttps://bioconductor.github.io/BiocWorkshops/ https://tess.elixir-europe.org/materials/bioc-2018-where-software-and-biology-connect Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Various authors Conference

Pitfalls and best practices for serializing Bioconductor objects

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Pitfalls and best practices for serializing Bioconductor objects https://bioconductor.org/help/course-materials/2019/BiocDevelForum/02-Serialization.pdf https://tess.elixir-europe.org/materials/pitfalls-and-best-practices-for-serializing-bioconductor-objects Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Lori Shepherd

Best Practices for Managing R / Bioconductor Scripts

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Best Practices

Best Practices for Managing R / Bioconductor Scripts https://bioconductor.org2014/summerx/BestPractices-slides.pdf https://tess.elixir-europe.org/materials/best-practices-for-managing-r-bioconductor-scripts Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Best Practices

Week 7: Participant stories

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workshop

Week 7: Participant stories https://bioconductor.orghttps://docs.google.com/document/d/1VCf1aOjW8BSrPO8Sf5m5rILWUYGdvdZNkZ0RwqVrkxs/edit https://tess.elixir-europe.org/materials/week-7-participant-stories Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Various Workshop

Week 5: Using AnVIL for teaching R / Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workshop

Week 5: Using AnVIL for teaching R / Bioconductor https://bioconductor.orghttps://docs.google.com/document/d/1fNNn3kleLrZLiXHsaUz7z2Et3kZ-IpIcBTlYzCYmscI/edit https://tess.elixir-europe.org/materials/week-5-using-anvil-for-teaching-r-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Levi Waldron Workshop

Week 6: Reproducible research with AnVILPublish

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workshop

Week 6: Reproducible research with AnVILPublish https://bioconductor.orghttps://docs.google.com/document/d/1KfAeZ4Tmg45AibOF8nugt7FnOo_KK6YFCTm13qYqoBI/edit https://tess.elixir-europe.org/materials/week-6-reproducible-research-with-anvilpublish Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Workshop

Week 4: Single-cell RNASeq with 'Orchestrating Single Cell Analysis' in R / Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workshop

Week 4: Single-cell RNASeq with 'Orchestrating Single Cell Analysis' in R / Bioconductor https://bioconductor.orghttps://docs.google.com/document/d/1xG_r7tcAy0RJm-ONI8uFHHHgNehd99hebUESSGQXAF4/edit https://tess.elixir-europe.org/materials/week-4-single-cell-rnaseq-with-orchestrating-single-cell-analysis-in-r-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Vince Carey Workshop

Genomic Ranges For Genome-Scale Data And Annotation

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Genomics

Genomic Ranges For Genome-Scale Data And Annotation https://bioconductor.org2015/Uruguay2015/V3-GenomicRanges.html https://tess.elixir-europe.org/materials/genomic-ranges-for-genome-scale-data-and-annotation Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Genomics

Translating R package documentation

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Translating R package documentation https://bioconductor.org2021/BiocDevelForum/23_Translating.pdf https://tess.elixir-europe.org/materials/translating-r-package-documentation Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

HCA / Bioconductor Seed Network Symposium

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

HCA / Bioconductor Seed Network Symposium https://bioconductor.orghttps://fast.wistia.com/embed/channel/jq84g71zlx?wchannelid=jq84g71zlx&wmediaid=uww7wikr4s https://tess.elixir-europe.org/materials/hca-bioconductor-seed-network-symposium Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Various

Analysis of RNA-Seq using the DESeq2 package

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

Analysis of RNA-Seq using the DESeq2 package https://bioconductor.org2014/BioC2014/RNA-Seq-Analysis-Lab.pdf https://tess.elixir-europe.org/materials/analysis-of-rna-seq-using-the-deseq2-package Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Michael Love RNA-Seq

Appendix: Install IGV

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Appendix

Appendix: Install IGV https://bioconductor.org2014/SeattleOct2014/D04.1_InstallIGV.html https://tess.elixir-europe.org/materials/appendix-install-igv Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Appendix

Introduction to linear models

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Introduction to linear models https://bioconductor.org2016/CSAMA/lect-04-linear-models/Waldron_linearmodels.pdf https://tess.elixir-europe.org/materials/introduction-to-linear-models Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Levi Waldron Statistics and probability

Gene set enrichment

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Gene set enrichment https://bioconductor.org2014/SeattleOct2014/B02.5_GeneSetEnrichment.html https://tess.elixir-europe.org/materials/gene-set-enrichment Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Gene-sets and correlation

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Gene-sets and correlation https://bioconductor.org2016/CSAMA/lect-17-gene-set-enrichment/gene_set_correlations.pdf https://tess.elixir-europe.org/materials/gene-sets-and-correlation Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Michael Love

Elements of statistics 5: experimental design

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Elements of statistics 5: experimental design https://bioconductor.org2014/CSAMA2014/5_Friday/lectures/ExpDesign_Anders.pdf https://tess.elixir-europe.org/materials/elements-of-statistics-5-experimental-design Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Simon Anders Statistics and probability

Elements of statistics 1: t-test and linear model

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Elements of statistics 1: t-test and linear model https://bioconductor.org2014/CSAMA2014/1_Monday/lectures/140623-gentleman-statistics-intro.pdf https://tess.elixir-europe.org/materials/elements-of-statistics-1-t-test-and-linear-model Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Robert Gentleman Statistics and probability

Bioconductor Masterclass: Bioconductor Essentials

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intro

Bioconductor Masterclass: Bioconductor Essentials https://bioconductor.org2017/BioCAsia/A01-Bioc-Basics.html https://tess.elixir-europe.org/materials/bioconductor-masterclass-bioconductor-essentials Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Intro

510: Maintaining your Bioconductor package

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Packages

510: Maintaining your Bioconductor package https://bioconductor.orghttps://bioconductor.github.io/BiocWorkshops/maintaining-your-bioconductor-package.html https://tess.elixir-europe.org/materials/510-maintaining-your-bioconductor-package Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Nitesh Turaga Packages

Developments in rhdf5

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Developments in rhdf5 https://bioconductor.orghttps://docs.google.com/presentation/d/1xWfHDw8pr65xDlKjM0PZLTWzOF7E0BPr1SD9s6kwDmM/edit#slide=id.p https://tess.elixir-europe.org/materials/developments-in-rhdf5 Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Mike Smith

102: Solving common bioinformatic challenges using GenomicRanges

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Genomics

102: Solving common bioinformatic challenges using GenomicRanges https://bioconductor.orghttps://bioconductor.github.io/BiocWorkshops/solving-common-bioinformatic-challenges-using-genomicranges.html https://tess.elixir-europe.org/materials/102-solving-common-bioinformatic-challenges-using-genomicranges Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Michael Lawrence Genomics

Sequence data represenations in Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Data Representation

Sequence data represenations in Bioconductor https://bioconductor.org2014/Epigenomics/SequenceDataRepresentation.html https://tess.elixir-europe.org/materials/sequence-data-represenations-in-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Data Representation

Multiple testing

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Multiple testing https://bioconductor.org/help/course-materials/2016/CSAMA/lect-02+13-testing/160711-brixen-testing-huber.pdf https://tess.elixir-europe.org/materials/hypothesis-testing-27ffb208-e582-48db-a8c0-ad22a87a1329 Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Wolfgang Huber Statistics and probability

Introduction to Bioconductor for Epigneomics

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Epigenomics

Introduction to Bioconductor for Epigneomics https://bioconductor.org2014/Epigenomics/BiocForEpigenomics.pdf https://tess.elixir-europe.org/materials/introduction-to-bioconductor-for-epigneomics Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Epigenomics

Robust statistics

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Robust statistics https://bioconductor.org2016/CSAMA/lect-11-robust/robust.pdf https://tess.elixir-europe.org/materials/robust-statistics Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Michael Love Statistics and probability

Working with DNA Sequences

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Data Representation

Working with DNA Sequences https://bioconductor.org/help/course-materials/2014/SeattleFeb2014/Bioconductor_sequences.pdf https://tess.elixir-europe.org/materials/genomic-ranges-slides Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Sonali Arora Data Representation

Counting Reads And Working With Large Files

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Large Data

Counting Reads And Working With Large Files https://bioconductor.org2015/Uruguay2015/V5-LargeFiles.html https://tess.elixir-europe.org/materials/counting-reads-and-working-with-large-files Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Large Data

Elements of statistics 4: regularisation & kernels

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Elements of statistics 4: regularisation & kernels https://bioconductor.org2014/CSAMA2014/4_Thursday/lectures/140626-brixen-machinelearn-huber.pdf https://tess.elixir-europe.org/materials/elements-of-statistics-4-regularisation-kernels Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Wolfgang Huber Statistics and probability

Visualization.

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Visualization. https://bioconductor.org2014/summerx/Visualization-slides.pdf https://tess.elixir-europe.org/materials/visualization-99cbbeae-48e4-40f5-bd49-50573bf35b1a Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Bioconductor annotations: using and sharing resources

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Bioconductor annotations: using and sharing resources https://bioconductor.org/help/workflows/annotation/annotation/ https://tess.elixir-europe.org/materials/bioconductor-annotations-using-and-sharing-resources Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Marc Carlson

Lab 9-1: Efficient and Parallel Evaluation

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Big data

Lab 9-1: Efficient and Parallel Evaluation https://bioconductor.org/help/course-materials/2019/CSAMA/L9.1-efficient-and-parallel-r.html https://tess.elixir-europe.org/materials/lab-9-1-efficient-and-parallel-evaluation Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Big data

Scalable Integrative Bioinformatics with Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Scalable Computing

Scalable Integrative Bioinformatics with Bioconductor https://bioconductor.org2014/ISMB2014/vjcScalable2.pptx https://tess.elixir-europe.org/materials/scalable-integrative-bioinformatics-with-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Vincent Carey Scalable Computing

Introduction to R

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: R

Introduction to R https://bioconductor.org2014/SeattleOct2014/A01.1_IntroductionToR.html https://tess.elixir-europe.org/materials/introduction-to-r-05a4bc85-7d88-4b09-aa40-8cf33e7b1af7 Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan R

Resampling methods

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Resampling methods https://bioconductor.org2016/CSAMA/lect-12-resampling/Waldron_CSAMA2016_resampling.pdf https://tess.elixir-europe.org/materials/resampling-methods Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Levi Waldron Statistics and probability

Understanding Bioconductor Annotation Packages

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Understanding Bioconductor Annotation Packages https://bioconductor.org2017/BioC2017/Day2/Workshops/Anno/doc/AnnotationWorkshop.html https://tess.elixir-europe.org/materials/understanding-bioconductor-annotation-packages Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. James MacDonald

Alternate Representations of R Objects or ALTREP

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Alternate Representations of R Objects or ALTREP https://bioconductor.org2020/BiocDevelForum/16-ALTREP.pdf https://tess.elixir-europe.org/materials/alternate-representations-of-r-objects-or-altrep Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Gabe Becker

06: Gene Set Enrichment -- Introduction

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intro

06: Gene Set Enrichment -- Introduction https://bioconductor.org/help/course-materials/2019/BSS2019/06_GeneSetEnrichmentSlides.pdf https://tess.elixir-europe.org/materials/06-gene-set-enrichment-introduction Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Intro

Google Hangout for New Package Submitters

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Best Practices

Google Hangout for New Package Submitters https://bioconductor.org2014/NewPackageHangout2014/PackageHangout.html https://tess.elixir-europe.org/materials/google-hangout-for-new-package-submitters Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Marc Carlson Best Practices

Introduction to Bioconductor for Sequence Analysis

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Sequence Analysis

Introduction to Bioconductor for Sequence Analysis https://bioconductor.org2014/Epigenomics/BiocForSequenceAnalysis.html https://tess.elixir-europe.org/materials/introduction-to-bioconductor-for-sequence-analysis Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Sequence Analysis

mbkmeans for clustering data with lots of samples

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

mbkmeans for clustering data with lots of samples https://bioconductor.orghttps://docs.google.com/presentation/d/1lMQ0A2lhUCNBabIl4HRKnKXMT5bb8-vJ5JcgYmeWGiI/edit#slide=id.p https://tess.elixir-europe.org/materials/mbkmeans-for-clustering-data-with-lots-of-samples Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Davide Risso

R / Bioconductor tools for mass spectrometry-based proteomics

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Proteomics

R / Bioconductor tools for mass spectrometry-based proteomics https://bioconductor.org2016/BioC2016/ConcurrentWorkshops4/Gatto/Bioc2016.html https://tess.elixir-europe.org/materials/r-bioconductor-tools-for-mass-spectrometry-based-proteomics Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Laurent Gatto Proteomics

BridgeDbR Tutorial

This tutorial describes how to use the BridgeDbR package for identifier mapping.

Keywords: ELIXIR RIR, BridgeDb

BridgeDbR Tutorial https://bioconductor.org/packages/devel/bioc/vignettes/BridgeDbR/inst/doc/tutorial.html https://tess.elixir-europe.org/materials/bridgedbr-tutorial-ce581787-b018-4a34-b161-5ed1b9cc8902 This tutorial describes how to use the BridgeDbR package for identifier mapping. Egon Willighagen ELIXIR RIR, BridgeDb

Managing big biological sequence data with Biostrings and DECIPHER

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Sequence Analysis

Managing big biological sequence data with Biostrings and DECIPHER https://bioconductor.org2016/BioC2016/ConcurrentWorkshops2/Wright/BigBioSeqData.pdf https://tess.elixir-europe.org/materials/managing-big-biological-sequence-data-with-biostrings-and-decipher Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Erik Wright Sequence Analysis

Analyzing splice events from RNA-seq data with SGSeq

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

Analyzing splice events from RNA-seq data with SGSeq https://bioconductor.org2016/BioC2016/ConcurrentWorkshops3/Goldstein/SGSeqBioC2016.html https://tess.elixir-europe.org/materials/analyzing-splice-events-from-rna-seq-data-with-sgseq Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Leonard Goldstein RNA-Seq

Copy Number

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Copy Number

Copy Number https://bioconductor.org2014/SeattleOct2014/B02.2.3_CopyNumber.html https://tess.elixir-europe.org/materials/copy-number Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Sonali Arora Copy Number

RNA-Seq Differential Expression

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

RNA-Seq Differential Expression https://bioconductor.org2015/Uruguay2015/V6-RNASeq.html https://tess.elixir-europe.org/materials/rna-seq-differential-expression Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan RNA-Seq

Sequence Data Representation

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Data Representation

Sequence Data Representation https://bioconductor.org2014/useR2014/DataRepresentation.html https://tess.elixir-europe.org/materials/sequence-data-representation Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Data Representation

Surprises from scalable container and cloud-based R / Bioconductor deployments

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Surprises from scalable container and cloud-based R / Bioconductor deployments https://bioconductor.orghttps://docs.google.com/presentation/d/e/2PACX-1vQUgyXDlkh1Kl91ICpudr9culyEuMSEppdi-qy97jwba3fy3m5UlKhJMvz_EW3JTP2Vu376OuzKcaQG/pub?start=false&loop=false&delayms=3000 https://tess.elixir-europe.org/materials/surprises-from-scalable-container-and-cloud-based-r-bioconductor-deployments Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

State of PCA

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

State of PCA https://bioconductor.orghttps://docs.google.com/presentation/d/1GNg1xIKNHU5eIEx01xpidpx4L_gFgBnk_ZCJnt4GEtk/edit#slide=id.p https://tess.elixir-europe.org/materials/state-of-pca Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Kasper Hansen

New Bioconductor packages for HCA Analysis

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

New Bioconductor packages for HCA Analysis https://bioconductor.orghttps://docs.google.com/presentation/d/1Xb8x3Cv6eibZM2zqxSFVBm6w_RBx8JitB3UtovaRq1Y/edit#slide=id.g4f2eea2032_0_48 https://tess.elixir-europe.org/materials/new-bioconductor-packages-for-hca-analysis Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Aaron Lun

Accessing Annotation Resources

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Accessing Annotation Resources https://bioconductor.org2014/ISMB2014/Annotation_slides.pdf https://tess.elixir-europe.org/materials/accessing-annotation-resources Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Working with DNA Sequences

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Data Representation

Working with DNA Sequences https://bioconductor.org2014/SeattleFeb2014/Bioconductor_sequences.pdf https://tess.elixir-europe.org/materials/genomic-ranges-slides-02149c9c-1bd0-4bdf-b1c6-784a084a2ccd Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Sonali Arora Data Representation

Variants

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Variants https://bioconductor.org2014/summerx/Variants-slides.pdf https://tess.elixir-europe.org/materials/variants Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Differential Gene Expression

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

Differential Gene Expression https://bioconductor.org2015/SeattleApr2015/C_DifferentialExpression.html https://tess.elixir-europe.org/materials/differential-gene-expression Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan RNA-Seq

Introduction to RNA-Seq data analysis

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

Introduction to RNA-Seq data analysis https://bioconductor.org2014/Epigenomics/RNASeqShortCourse.pdf https://tess.elixir-europe.org/materials/introduction-to-rna-seq-data-analysis Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Benilton Carvalho RNA-Seq

Elements of statistics 3: Classification and clustering - basic concepts

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Elements of statistics 3: Classification and clustering - basic concepts https://bioconductor.org2014/CSAMA2014/4_Thursday/lectures/thursClust.html https://tess.elixir-europe.org/materials/elements-of-statistics-3-classification-and-clustering-basic-concepts Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Unknown Statistics and probability

Introduction to R (slides)

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: R

Introduction to R (slides) https://bioconductor.org2014/Epigenomics/IntroductionToR.html https://tess.elixir-europe.org/materials/introduction-to-r-slides Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan R

Bioconductor - Slides

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: R/Bioconductor

Bioconductor - Slides https://bioconductor.org2014/SeattleFeb2014/Bioconductor_slides.pdf https://tess.elixir-europe.org/materials/bioconductor-slides Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan R/Bioconductor

A short methylation analysis using minfi

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

A short methylation analysis using minfi https://bioconductor.org2014/Epigenomics/MethylationArrays-lab.html https://tess.elixir-europe.org/materials/a-short-methylation-analysis-using-minfi Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Gene set enrichment analysis

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Gene set enrichment analysis https://bioconductor.org2014/CSAMA2014/3_Wednesday/lectures/GSEA2014.pdf https://tess.elixir-europe.org/materials/gene-set-enrichment-analysis Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Robert Gentleman

02: Practical: R / Bioconductor and Reproducible Research

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intro

02: Practical: R / Bioconductor and Reproducible Research https://bioconductor.org/help/course-materials/2019/BSS2019/02_Practical_RBioconductorAndReproductibleResearch.html https://tess.elixir-europe.org/materials/02-practical-r-bioconductor-and-reproducible-research Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Intro

Day 2 European Bioconductor Meeting 2017

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Conference

Day 2 European Bioconductor Meeting 2017 https://bioconductor.orghttps://www.youtube.com/watch?v=dfYF0lAeV_Y&t=1s https://tess.elixir-europe.org/materials/day-2-european-bioconductor-meeting-2017 Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Various authors Conference

The Bioconductor Project: Current Status

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Status

Resource type: Talk

The Bioconductor Project: Current Status https://bioconductor.org2016/BiocAsia/Talk.pdf https://tess.elixir-europe.org/materials/the-bioconductor-project-current-status Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Status

Visualisation and assessment of ChIP-seq quality using ChIPQC and Diffbind packages

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: ChIP-seq

Visualisation and assessment of ChIP-seq quality using ChIPQC and Diffbind packages https://bioconductor.org2014/BioC2014/Bioc2014_ChIPQC_Practical.pdf https://tess.elixir-europe.org/materials/visualisation-and-assessment-of-chip-seq-quality-using-chipqc-and-diffbind-packages Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Tom Carroll ChIP-seq

Lecture: Introduction to MS based proteomics and Bioconductor infrastructure

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Proteomics

Lecture: Introduction to MS based proteomics and Bioconductor infrastructure https://bioconductor.org2015/CSAMA2015/lect/L10-proteomics-gatto.pdf https://tess.elixir-europe.org/materials/lecture-introduction-to-ms-based-proteomics-and-bioconductor-infrastructure Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Laurent Gatto Proteomics

Variant calling with Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Variant calling with Bioconductor https://bioconductor.org2014/BioC2014/Lawrence_Tutorial.pdf https://tess.elixir-europe.org/materials/variant-calling-with-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Michael Lawrence

Lab: Performance and Parallel Evaluation

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: LargeData

Lab: Performance and Parallel Evaluation https://bioconductor.org2015/CSAMA2015/lab/L7-performance-and-large-data-morgan.html https://tess.elixir-europe.org/materials/lab-performance-and-parallel-evaluation Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan LargeData

Multiple testing

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Multiple testing https://bioconductor.org2016/CSAMA/lect-02+13-testing/160711-brixen-testing-huber.pdf https://tess.elixir-europe.org/materials/hypothesis-testing-5b272664-09d5-44b0-b6c4-7ff60ad2a762 Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Wolfgang Huber Statistics and probability

What should you do next?

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intermediate

What should you do next? https://bioconductor.org2016/CSAMA/lect-20-what-now/2016-07_next-steps-csama.pdf https://tess.elixir-europe.org/materials/what-should-you-do-next Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Jenny Bryan Intermediate

Lab 1: Introduction to R and Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: introduction

Lab 1: Introduction to R and Bioconductor https://bioconductor.org/help/course-materials/2019/CSAMA/lab-1-intro-to-r-bioc.html https://tess.elixir-europe.org/materials/lab-1-introduction-to-r-and-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan introduction

Supplement 1: RNA-Seq Workflow

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

Supplement 1: RNA-Seq Workflow https://bioconductor.org2015/Uruguay2015/S1-RNASeq-Workflow.html https://tess.elixir-europe.org/materials/supplement-1-rna-seq-workflow Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan RNA-Seq

DNA-Seq 1: Variant calling

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Sequencing

DNA-Seq 1: Variant calling https://bioconductor.org2014/CSAMA2014/3_Wednesday/lectures/VariantCallingLecture.pdf https://tess.elixir-europe.org/materials/dna-seq-1-variant-calling Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Michael Lawrence Sequencing

Analysis of 450k methylation data with the minfi package

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Analysis of 450k methylation data with the minfi package https://bioconductor.org2014/BioC2014/minfi_BioC2014.pdf https://tess.elixir-europe.org/materials/analysis-of-450k-methylation-data-with-the-minfi-package Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Kasper Hansen

Hello Ranges: An Introduction to Analyzing Genomic Ranges in R

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Genomics

Hello Ranges: An Introduction to Analyzing Genomic Ranges in R https://bioconductor.org2016/BioC2016/ConcurrentWorkshops3/Lawrence/tutorial.pdf https://tess.elixir-europe.org/materials/hello-ranges-an-introduction-to-analyzing-genomic-ranges-in-r Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Michael Lawrence Genomics

RNA-Seq 1: differential expression analysis - GLMs and testing

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

RNA-Seq 1: differential expression analysis - GLMs and testing https://bioconductor.org2014/CSAMA2014/2_Tuesday/lectures/DESeq2-Anders.pdf https://tess.elixir-europe.org/materials/rna-seq-1-differential-expression-analysis-glms-and-testing Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Simon Anders RNA-Seq

Bioconductor updates

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Bioconductor updates https://bioconductor.orghttps://docs.google.com/presentation/d/e/2PACX-1vSDB3BZ711d7-2yoCZmd_2MgcNeAlZyGNOIFyVSRPvZmu2Z887alznon0J8RW6O5towyJdjoUbvoL0D/pub https://tess.elixir-europe.org/materials/bioconductor-updates Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Lecture: Computing with sequences and genomic intervals

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: GenomicRanges

Lecture: Computing with sequences and genomic intervals https://bioconductor.org2015/CSAMA2015/lect/L07-sequences-ranges-morgan.pdf https://tess.elixir-europe.org/materials/lecture-computing-with-sequences-and-genomic-intervals Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan GenomicRanges

eQTL analysis -- an approach with Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: eQTL

eQTL analysis -- an approach with Bioconductor https://bioconductor.org2014/Epigenomics/eQTLtalk.pdf https://tess.elixir-europe.org/materials/eqtl-analysis-an-approach-with-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Vincent Carey eQTL

Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: R/Bioconductor

Bioconductor https://bioconductor.org2014/summerx/Bioconductor-slides.pdf https://tess.elixir-europe.org/materials/bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan R/Bioconductor

Say Hello to ALTREP

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Say Hello to ALTREP https://bioconductor.org2020/BiocDevelForum/17-ALTREP2.pdf https://tess.elixir-europe.org/materials/say-hello-to-altrep Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Jiefei Wang

BiocCheck-a-thon check in

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

BiocCheck-a-thon check in https://bioconductor.orghttps://www.youtube.com/watch?v=SilmcI8WlMM&t=5s https://tess.elixir-europe.org/materials/bioccheck-a-thon-check-in Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Various

Cancer Immuno-Oncology: Bioconductor and beyond

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workshop

Cancer Immuno-Oncology: Bioconductor and beyond https://bioconductor.org2019/CMCM/01-Workshop.Rmd https://tess.elixir-europe.org/materials/cancer-immuno-oncology-bioconductor-and-beyond Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Workshop

Adding Annotation To Your Analysis

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Adding Annotation To Your Analysis https://bioconductor.org2015/Uruguay2015/V4-Annotation.html https://tess.elixir-europe.org/materials/adding-annotation-to-your-analysis Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

R / Bioconductor for everyone

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: R/Bioconductor

R / Bioconductor for everyone https://bioconductor.org2014/BioC2014/RBiocForEveryone.pdf https://tess.elixir-europe.org/materials/r-bioconductor-for-everyone Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan R/Bioconductor

RNA-Seq

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

RNA-Seq https://bioconductor.org2014/SeattleOct2014/B02.1_RNASeq.html https://tess.elixir-europe.org/materials/rna-seq-387b1419-9068-4001-b32b-e43a513034c7 Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan RNA-Seq

eQTL / molecular-QTL analyses

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: eQTL / molecular-QTL

eQTL / molecular-QTL analyses https://bioconductor.org2014/CSAMA2014/5_Friday/lectures/vjcEQTLfri.pdf https://tess.elixir-europe.org/materials/eqtl-molecular-qtl-analyses Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Vincent Carey eQTL / molecular-QTL

Counting reads for RNA-seq in Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

Counting reads for RNA-seq in Bioconductor https://bioconductor.org2014/Epigenomics/CountingReadsForRNASeq.pdf https://tess.elixir-europe.org/materials/counting-reads-for-rna-seq-in-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan RNA-Seq

Introduction to working with methylation arrays (slides)

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Introduction to working with methylation arrays (slides) https://bioconductor.org2014/Epigenomics/MethylationArrays.html https://tess.elixir-europe.org/materials/introduction-to-working-with-methylation-arrays-slides Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Working with Large Data

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Large Data

Working with Large Data https://bioconductor.org2014/SeattleOct2014/C03.1_LargeData.html https://tess.elixir-europe.org/materials/working-with-large-data Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Large Data

Analysis of RNA-Seq Data

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

Analysis of RNA-Seq Data https://bioconductor.orghttp://mikelove.github.io/biocrnaseq/#1 https://tess.elixir-europe.org/materials/analysis-of-rna-seq-data Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Mike Love RNA-Seq

Lecture: RNA-Seq data analysis and differential expression part I

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

Lecture: RNA-Seq data analysis and differential expression part I https://bioconductor.org2015/CSAMA2015/lect/L05-deseq2-anders.pdf https://tess.elixir-europe.org/materials/lecture-rna-seq-data-analysis-and-differential-expression-part-i Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Simon Anders RNA-Seq

ChIP-seq with csaw

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: ChIP-seq

ChIP-seq with csaw https://bioconductor.org2015/SeattleApr2015/F_ChIPSeq.html https://tess.elixir-europe.org/materials/chip-seq-with-csaw Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan ChIP-seq

R / Bioconductor packages for Proteomics

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Proteomics

R / Bioconductor packages for Proteomics https://bioconductor.org2014/BioC2014/Gatto.html https://tess.elixir-europe.org/materials/r-bioconductor-packages-for-proteomics Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Laurent Gatto Proteomics

High-throughput sequencing: Alignment and related topic

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

High-throughput sequencing: Alignment and related topic https://bioconductor.org2014/CSAMA2014/1_Monday/lectures/HTS_intro__Anders.pdf https://tess.elixir-europe.org/materials/high-throughput-sequencing-alignment-and-related-topic Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Simon Anders RNA-Seq

Visualization

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Visualization https://bioconductor.org2014/SeattleOct2014/C03.4_Visualization.html https://tess.elixir-europe.org/materials/visualization Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Genetics of gene expression: computation and integrative prediction

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: eQTL

Genetics of gene expression: computation and integrative prediction https://bioconductor.org2014/BioC2014/eqtl2014.html https://tess.elixir-europe.org/materials/genetics-of-gene-expression-computation-and-integrative-prediction Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Vincent Carey eQTL

Liftr & sbgr

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workflows

Liftr & sbgr https://bioconductor.org/BioC2015/#ami https://tess.elixir-europe.org/materials/detecting-differential-binding-in-chip-seq-data-with-csaw-7a3a67bf-a44b-4bcb-a54f-02412e71104c Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Nan Xiao Workflows

Introduction

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Introduction https://bioconductor.org2020/HCASymposium/01-Introduction.pdf https://tess.elixir-europe.org/materials/introduction-e309609e-264f-4023-9485-f406549bb597 Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Working with Annotations

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Working with Annotations https://bioconductor.org2014/SeattleFeb2014/Annotation.pdf https://tess.elixir-europe.org/materials/working-with-annotations Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

ChIP-seq Analysis

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: ChIP-seq

ChIP-seq Analysis https://bioconductor.org2014/CSAMA2014/4_Thursday/lectures/ChIPSeq_slides.pdf https://tess.elixir-europe.org/materials/chip-seq-analysis-a09e63fd-d145-4eb1-af5b-30127d21f15e Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan ChIP-seq

Learn how to use Bioconductor to perform common tasks on your high-throughput sequencing data

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Genomics

Learn how to use Bioconductor to perform common tasks on your high-throughput sequencing data https://bioconductor.org2014/BioC2014/GenomicRangesHOWTOs.pdf https://tess.elixir-europe.org/materials/learn-how-to-use-bioconductor-to-perform-common-tasks-on-your-high-throughput-sequencing-data Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Hervé Pagès Genomics

Lecture: Clustering and classification

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Lecture: Clustering and classification https://bioconductor.org2015/CSAMA2015/lect/L04-clusclass-carey.html https://tess.elixir-europe.org/materials/lecture-clustering-and-classification Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Vincent Carey Statistics and probability

RNASeq Analysis

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

RNASeq Analysis https://bioconductor.org2014/SeattleFeb2014/RNASeq.pdf https://tess.elixir-europe.org/materials/rnaseq-analysis Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Introduction to Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Bioconductor

Introduction to Bioconductor https://bioconductor.org2014/SeattleOct2014/A01.2_IntroductionToBioconductor.html https://tess.elixir-europe.org/materials/introduction-to-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Bioconductor

Outreach

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Outreach https://bioconductor.org2020/HCASymposium/05-OutreachChallengesAndOpportunities.pdf https://tess.elixir-europe.org/materials/outreach Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Stephanie Hicks

ChIP-Seq analysis basics

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: ChIP-seq

ChIP-Seq analysis basics https://bioconductor.org2016/CSAMA/lab-5-chipseq/Epigenetics.Rmd https://tess.elixir-europe.org/materials/chip-seq-analysis-basics Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Alejandro Reyes; Mike Smith ChIP-seq

HCAMatrixBrowser for retrieving count matrices

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

HCAMatrixBrowser for retrieving count matrices https://bioconductor.orghttps://www.youtube.com/watch?v=fCFvS0Ze5W4 https://tess.elixir-europe.org/materials/hcamatrixbrowser-for-retrieving-count-matrices Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Marcel Ramos

Liftr & sbgr

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workflows

Liftr & sbgr https://bioconductor.org/help/course-materials//BioC2015/#ami https://tess.elixir-europe.org/materials/detecting-differential-binding-in-chip-seq-data-with-csaw Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Nan Xiao Workflows

R / Bioconductor for 'Omics Analysis (U. Idaho)

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Overview

R / Bioconductor for 'Omics Analysis (U. Idaho) https://bioconductor.org2017/UIdaho/Overview.pdf https://tess.elixir-europe.org/materials/r-bioconductor-for-omics-analysis-u-idaho Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Overview

Meta-analysis of genomics experiments using Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Meta-analysis

Meta-analysis of genomics experiments using Bioconductor https://bioconductor.orghttp://rpubs.com/lwaldron/bioc2014 https://tess.elixir-europe.org/materials/meta-analysis-of-genomics-experiments-using-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Levi Waldron Meta-analysis

Ranges

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Genomics

Ranges https://bioconductor.org2014/summerx/Ranges-slides.pdf https://tess.elixir-europe.org/materials/ranges Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Hervé Pagès Genomics

ChIP-Seq for Understanding Gene Regulation

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: ChIP-seq

ChIP-Seq for Understanding Gene Regulation https://bioconductor.org2015/Uruguay2015/V7-ChIPSeq.html https://tess.elixir-europe.org/materials/chip-seq-for-understanding-gene-regulation Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan ChIP-seq

Trends in Genomic Data Analysis in R

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: R/Bioconductor

Trends in Genomic Data Analysis in R https://bioconductor.org2014/ISMB2014/ISMB2014_WaldronOverview.pdf https://tess.elixir-europe.org/materials/trends-in-genomic-data-analysis-in-r Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Levi Waldron R/Bioconductor

Parallel Computing with Bioconductor in the Amazon Cloud

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Scalable Computing

Parallel Computing with Bioconductor in the Amazon Cloud https://bioconductor.org2014/BioC2014/ParallelBioc.pdf https://tess.elixir-europe.org/materials/parallel-computing-with-bioconductor-in-the-amazon-cloud Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Valerie Obenchain Scalable Computing

Update from EuroBioc2019 user/developer sessions

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Update from EuroBioc2019 user/developer sessions https://bioconductor.org2019/BiocDevelForum/05-EuroBioc.pdf https://tess.elixir-europe.org/materials/update-from-eurobioc2019-user-developer-sessions Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Various authors

500: Effectively using the DelayedArray framework to support the analysis of large datasets

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Large data

500: Effectively using the DelayedArray framework to support the analysis of large datasets https://bioconductor.orghttps://bioconductor.github.io/BiocWorkshops/effectively-using-the-delayedarray-framework-to-support-the-analysis-of-large-datasets.html https://tess.elixir-europe.org/materials/500-effectively-using-the-delayedarray-framework-to-support-the-analysis-of-large-datasets Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Pete Hickey Large data

Lecture: Epigenetics and ChIP-Seq

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: ChIP-seq

Lecture: Epigenetics and ChIP-Seq https://bioconductor.org2015/CSAMA2015/lect/L08-epigenetics-and-chip-seq-pekowska.pdf https://tess.elixir-europe.org/materials/lecture-epigenetics-and-chip-seq Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Aleksandra Pȩkowska ChIP-seq

Lecture 20-1: Working with Large Data

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Big data

Lecture 20-1: Working with Large Data https://bioconductor.org/help/course-materials/2019/CSAMA/lecture-20-1-big-data.html https://tess.elixir-europe.org/materials/lecture-20-1-working-with-large-data Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Big data

Lecture: Hypothesis testing and multiple testing

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Lecture: Hypothesis testing and multiple testing https://bioconductor.org2015/CSAMA2015/lect/L03-testing-huber.pdf https://tess.elixir-europe.org/materials/lecture-hypothesis-testing-and-multiple-testing Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Wolfgang Huber Statistics and probability

R7 for Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

R7 for Bioconductor https://bioconductor.org2021/BiocDevelForum/20-R7.pdf https://tess.elixir-europe.org/materials/r7-for-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Michael Lawrence

Supplement 2: RNA-Seq Statistical Issues

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

Supplement 2: RNA-Seq Statistical Issues https://bioconductor.org2015/Uruguay2015/S2-RNASeq-Experimental-Design.html https://tess.elixir-europe.org/materials/supplement-2-rna-seq-statistical-issues Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan RNA-Seq

Lab: Plotting Regions from BAM files directly

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Lab: Plotting Regions from BAM files directly https://bioconductor.org2015/CSAMA2015/lab/Paul.Pyl.Plotting.Variants.or.Ranges.from.Bam.files.directly.html https://tess.elixir-europe.org/materials/lab-plotting-regions-from-bam-files-directly Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Paul Pyl

Work flows : RNA-Seq

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

Work flows : RNA-Seq https://bioconductor.org2014/useR2014/Workflows.html https://tess.elixir-europe.org/materials/work-flows-rna-seq Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan RNA-Seq

R Graphics

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Graphics

R Graphics https://bioconductor.org2016/CSAMA/lab-8-graphics/graphics-chapter.Rmd https://tess.elixir-europe.org/materials/r-graphics Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Wolfgang Huber Graphics

Introduction to new package development and submission

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Packages

Introduction to new package development and submission https://bioconductor.org2017/BioC2017/DDay/Workshop/MakeAPackage.html https://tess.elixir-europe.org/materials/introduction-to-new-package-development-and-submission Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Lori Shepherd Packages

Bioconductor and R 4.0

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Bioconductor and R 4.0 https://bioconductor.org2020/BiocDevelForum/08-Rdevel.pdf https://tess.elixir-europe.org/materials/bioconductor-and-r-4-0 Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Lori Shepherd

An RNA-seq work flow

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: RNAseq

An RNA-seq work flow https://bioconductor.org2016/BKU/S4_RNASeq.html https://tess.elixir-europe.org/materials/an-rna-seq-work-flow Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan RNAseq

Introduction to Bayesian Inference using Stan with Applications to Cancer Genomics

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Introduction to Bayesian Inference using Stan with Applications to Cancer Genomics https://bioconductor.org2016/BioC2016/ConcurrentWorkshops4/Buros/applied-survival-model.html https://tess.elixir-europe.org/materials/introduction-to-bayesian-inference-using-stan-with-applications-to-cancer-genomics Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Jacqueline Buros Statistics and probability

End-to-end RNA-Seq workflow

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: RNAseq

End-to-end RNA-Seq workflow https://bioconductor.org2016/CSAMA/lab-3-rnaseq/rnaseq_gene_CSAMA2016.Rmd https://tess.elixir-europe.org/materials/end-to-end-rna-seq-workflow Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Simon Anders; Michael Love; Charlotte Soneson RNAseq

Annotating high throughput data using Bioconductor resources

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Annotating high throughput data using Bioconductor resources https://bioconductor.org2016/BioC2016/ConcurrentWorkshops2/MacDonald/AnnotationWorkshop.html https://tess.elixir-europe.org/materials/annotating-high-throughput-data-using-bioconductor-resources Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. James MacDonald

RNA-seq data analysis and differential expression

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: RNAseq

RNA-seq data analysis and differential expression https://bioconductor.org2016/CSAMA/lect-06-rnaseq-analysis/rnaseq.pdf https://tess.elixir-europe.org/materials/rna-seq-data-analysis-and-differential-expression Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Michael Love RNAseq

Visualisation in Statistical Genomics

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Visualisation in Statistical Genomics https://bioconductor.org2014/CSAMA2014/2_Tuesday/lectures/Visualization_in_Statistical_Genomics-Carey.pdf https://tess.elixir-europe.org/materials/visualisation-in-statistical-genomics Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Vincent Carey

Introduction to R / Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: R/Bioconductor

Introduction to R / Bioconductor https://bioconductor.org2014/useR2014/Introduction.html https://tess.elixir-europe.org/materials/introduction-to-r-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan R/Bioconductor

Lecture: RNA-Seq data analysis and differential expression part II

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

Lecture: RNA-Seq data analysis and differential expression part II https://bioconductor.org2015/CSAMA2015/lect/L06-rna-stats-love.pdf https://tess.elixir-europe.org/materials/lecture-rna-seq-data-analysis-and-differential-expression-part-ii Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Michael Love RNA-Seq

Genomic Ranges

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Genomics

Genomic Ranges https://bioconductor.org2015/SeattleApr2015/B_GenomicRanges.html https://tess.elixir-europe.org/materials/genomic-ranges Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Genomics

DNA-Seq 2: visualisation and quality assessment of variant calls

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Sequencing

DNA-Seq 2: visualisation and quality assessment of variant calls https://bioconductor.org2014/CSAMA2014/3_Wednesday/lectures/CSAMA2014.variant.visualisation.and.qc.pdf https://tess.elixir-europe.org/materials/dna-seq-2-visualisation-and-quality-assessment-of-variant-calls Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Paul Theodor Pyl Sequencing

Independent Hypothesis Weighting

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Independent Hypothesis Weighting https://bioconductor.org2016/CSAMA/lab-6-hypothesis-weighting/introduction_to_ihw.Rmd https://tess.elixir-europe.org/materials/independent-hypothesis-weighting Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Wolfgang Huber Statistics and probability

Lab: Reproducible Research and R Authoring with markdown and knitr

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: ReproducibleResearch

Lab: Reproducible Research and R Authoring with markdown and knitr https://bioconductor.org2015/CSAMA2015/lab/rr-authoring.html https://tess.elixir-europe.org/materials/lab-reproducible-research-and-r-authoring-with-markdown-and-knitr Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Laurent Gatto ReproducibleResearch

Integrative Data Analysis

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Large Data

Integrative Data Analysis https://bioconductor.org2015/SeattleApr2015/H_IntegrativeAnalysis.html https://tess.elixir-europe.org/materials/integrative-data-analysis Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Large Data

Working with Data: SummarizedExperiment

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: SummarizedExperiment

Working with Data: SummarizedExperiment https://bioconductor.org2015/Uruguay2015/V2-WorkingWithData.html https://tess.elixir-europe.org/materials/working-with-data-summarizedexperiment Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan SummarizedExperiment

The TCGAbiolinks package

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Data Integration

The TCGAbiolinks package https://bioconductor.org2015/Uruguay2015/TCGAbiolinks.pdf https://tess.elixir-europe.org/materials/the-tcgabiolinks-package Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Houtan Noushmehr Data Integration

Common Sequence Analysis Work Flows

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workflows

Common Sequence Analysis Work Flows https://bioconductor.org2014/SeattleOct2014/B02.2_CommonWorkFlows.html https://tess.elixir-europe.org/materials/common-sequence-analysis-work-flows Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Workflows

Lab: Phyloseq Basic Usage for Metagenomics

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Metagenomics

Lab: Phyloseq Basic Usage for Metagenomics https://bioconductor.org2015/CSAMA2015/lab/Paul.Pyl.Phyloseq.Basics.html https://tess.elixir-europe.org/materials/lab-phyloseq-basic-usage-for-metagenomics Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Paul Pyl Metagenomics

Working with gene and genome annotations

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Working with gene and genome annotations https://bioconductor.org2014/CSAMA2014/3_Wednesday/lectures/Annotation_slides.pdf https://tess.elixir-europe.org/materials/working-with-gene-and-genome-annotations Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Visualization of Genomic Data

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

Visualization of Genomic Data https://bioconductor.org2014/SeattleFeb2014/Visualization.pdf https://tess.elixir-europe.org/materials/visualization-of-genomic-data Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Sonali Arora RNA-Seq

Workshop: RNASeq

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

Workshop: RNASeq https://bioconductor.org2015/BiocAsia2015/#ami https://tess.elixir-europe.org/materials/workshop-rnaseq Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan RNA-Seq

HCA Data Access

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

HCA Data Access https://bioconductor.org/help/course-materials/2019/HCA/HCA_Data_Access.pptx https://tess.elixir-europe.org/materials/hca-data-access Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Daniel van Twisk

Microbial genomics

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Microbiome

Microbial genomics https://bioconductor.org2016/CSAMA/lect-15-microbiome/microbiome.pdf https://tess.elixir-europe.org/materials/microbial-genomics Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Charlotte Soneson Microbiome

Gene Expression

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Microarrays

Gene Expression https://bioconductor.org2015/Uruguay2015/day3-gene.expression.html https://tess.elixir-europe.org/materials/gene-expression Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Houtan Noushmehr Microarrays

03: Core approaches in Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intro

03: Core approaches in Bioconductor https://bioconductor.org/help/course-materials/2019/BSS2019/03_CoreApproachesInBioconductor.html https://tess.elixir-europe.org/materials/03-core-approaches-in-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Intro

CRISPRseek: Design of target-specific guide RNAs in CRISPR-Cas9 genome-editing systems

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

CRISPRseek: Design of target-specific guide RNAs in CRISPR-Cas9 genome-editing systems https://bioconductor.org2014/BioC2014/CRISPRseek-forBioc2014.pdf https://tess.elixir-europe.org/materials/crisprseek-design-of-target-specific-guide-rnas-in-crispr-cas9-genome-editing-systems Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Julie Zhu RNA-Seq

Ontology issues

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Ontology issues https://bioconductor.orghttps://docs.google.com/presentation/d/1VUWJeFv27OKSU9YNA2tqNW5QX9ViGF_12-CHFJXmMCA/edit#slide=id.p https://tess.elixir-europe.org/materials/ontology-issues Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Vincent Carey

Meta-analysis

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Statistics and probability

Meta-analysis https://bioconductor.org2016/CSAMA/lect-18-meta-analysis/Waldron_metaanalysis.pdf https://tess.elixir-europe.org/materials/meta-analysis Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Levi Waldron Statistics and probability

How Bioconductor advances science and contributes to R

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Keynote

How Bioconductor advances science and contributes to R https://bioconductor.orghttps://docs.google.com/presentation/d/e/2PACX-1vQnSGdSu3iSrVTZadiuOEXXrnikX7qS_A4NBHDbNxVMojPy69zu_dLwWH5pjAb1chY4Jz5n74y72Q4z/pub?start=false&loop=false&delayms=3000 https://tess.elixir-europe.org/materials/how-bioconductor-advances-science-and-contributes-to-r Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Keynote

Reproducible research and R authoring with markdown and knitr

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Git

Reproducible research and R authoring with markdown and knitr https://bioconductor.orghttps://github.com/jennybc/happy-git-with-r https://tess.elixir-europe.org/materials/reproducible-research-and-r-authoring-with-markdown-and-knitr Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Jenny Bryan Git

High-throughput sequencing and using short-read aligners

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Sequencing

High-throughput sequencing and using short-read aligners https://bioconductor.org2016/CSAMA/lect-05-aligning/Anders_aligners.pdf https://tess.elixir-europe.org/materials/high-throughput-sequencing-and-using-short-read-aligners Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Simon Anders Sequencing

Bioconductor for 'Omics Analysis (University of Rochester Medical Center)

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Overview

Bioconductor for 'Omics Analysis (University of Rochester Medical Center) https://bioconductor.org2016/Rochester/Overview.pdf https://tess.elixir-europe.org/materials/bioconductor-for-omics-analysis-university-of-rochester-medical-center Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Overview

06: Gene Set Enrichment Analysis

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intro

06: Gene Set Enrichment Analysis https://bioconductor.org/help/course-materials/2019/BSS2019/06_GeneSetEnrichment.html https://tess.elixir-europe.org/materials/06-gene-set-enrichment-analysis Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Intro

Proteomics

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Proteomics

Proteomics https://bioconductor.org2014/CSAMA2014/5_Friday/lectures/proteomics_slides.pdf https://tess.elixir-europe.org/materials/proteomics Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Laurent Gatto Proteomics

Improving findability of BioC packages

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Improving findability of BioC packages https://bioconductor.org2019/BiocDevelForum/04-Findability.pdf https://tess.elixir-europe.org/materials/improving-findability-of-bioc-packages Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Steffen Neumann

Lab: Interactive data visualization with Shiny

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Lab: Interactive data visualization with Shiny https://bioconductor.org2015/CSAMA2015/lab/shiny.html https://tess.elixir-europe.org/materials/lab-interactive-data-visualization-with-shiny Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Andrzej Oleś

Integrated pathway analysis of multiple omics datasets

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Pathway

Integrated pathway analysis of multiple omics datasets https://bioconductor.org2014/BioC2014/IntAnalysis.html https://tess.elixir-europe.org/materials/integrated-pathway-analysis-of-multiple-omics-datasets Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Aedin Culhane Pathway

250: Working with genomic data in R with the DECIPHER package

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Genomic data

250: Working with genomic data in R with the DECIPHER package https://bioconductor.orghttps://bioconductor.github.io/BiocWorkshops/working-with-genomic-data-in-r-with-the-decipher-package.html https://tess.elixir-europe.org/materials/250-working-with-genomic-data-in-r-with-the-decipher-package Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Nicholas Cooley Genomic data

Building and running automated NGS analysis workflows

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: workflows

Building and running automated NGS analysis workflows https://bioconductor.org2016/BioC2016/ConcurrentWorkshops1/Girke/systemPipeR_Intro.html https://tess.elixir-europe.org/materials/building-and-running-automated-ngs-analysis-workflows Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Thomas Girke workflows

Lecture: Basics of sequence alignment and aligners

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Technology

Lecture: Basics of sequence alignment and aligners https://bioconductor.org2015/CSAMA2015/lect/L02-hts-intro-anders.pdf https://tess.elixir-europe.org/materials/lecture-basics-of-sequence-alignment-and-aligners Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Simon Anders Technology

Reproducible Research

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Reproducibility

Reproducible Research https://bioconductor.org2014/SeattleOct2014/C03.3_ReproducibleResearch.html https://tess.elixir-europe.org/materials/reproducible-research Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Reproducibility

Large Data

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Large Data

Large Data https://bioconductor.org2015/SeattleApr2015/I_LargeData.html https://tess.elixir-europe.org/materials/large-data Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Large Data

Conducting Genomic Symphonies with Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Conducting Genomic Symphonies with Bioconductor https://bioconductor.org2017/BioInfoSummer/bioc-bioinfosummer-2017.pdf https://tess.elixir-europe.org/materials/conducting-genomic-symphonies-with-bioconductor Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Michael Lawrence

Ensembl gene set enrichment analysis with EGSEA

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Enrichment

Ensembl gene set enrichment analysis with EGSEA https://bioconductor.org2017/BioC2017/Day2/Workshops/EGSEA/doc/EGSEAWorkflow.html https://tess.elixir-europe.org/materials/ensembl-gene-set-enrichment-analysis-with-egsea Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Matt Ritchie Enrichment

Computing with sequences and ranges

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: Genomics

Computing with sequences and ranges https://bioconductor.org2016/CSAMA/lect-08-sequences-and-ranges/lect-08-sequences-and-ranges.pdf https://tess.elixir-europe.org/materials/computing-with-sequences-and-ranges Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Genomics

05: Bioconductor Annotation Resources

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intro

05: Bioconductor Annotation Resources https://bioconductor.org/help/course-materials/2019/BSS2019/05_Annotations.html https://tess.elixir-europe.org/materials/05-bioconductor-annotation-resources Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Intro

Graphics

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Graphics

Graphics https://bioconductor.org2016/CSAMA/lect-16-graphics/160714-brixen-viz-huber.pdf https://tess.elixir-europe.org/materials/graphics Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Wolfgang Huber Graphics

HCABrowser for discovery and access

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

HCABrowser for discovery and access https://bioconductor.orghttps://www.youtube.com/watch?v=BqQDmdtvVSk https://tess.elixir-europe.org/materials/hcabrowser-for-discovery-and-access Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Daniel van Twisk

Bioconductor Masterclass: Package Development

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Devel

Bioconductor Masterclass: Package Development https://bioconductor.org2017/BioCAsia/A02-Package-Development.html https://tess.elixir-europe.org/materials/bioconductor-masterclass-package-development Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Devel

RNA-Seq 3: alternative exon usage

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

RNA-Seq 3: alternative exon usage https://bioconductor.org2014/CSAMA2014/4_Thursday/lectures/isoforms_dexseq_talk.pdf https://tess.elixir-europe.org/materials/rna-seq-3-alternative-exon-usage Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Alejandro Reyes RNA-Seq

R packages for communicating reproducible research

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Workshop

R packages for communicating reproducible research https://bioconductor.org2019/IISA/RPackages.html https://tess.elixir-europe.org/materials/r-packages-for-communicating-reproducible-research Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Workshop

Adding additional compression filters to rhdf5

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Adding additional compression filters to rhdf5 https://bioconductor.org2019/BiocDevelForum/05-rhdf5.pdf https://tess.elixir-europe.org/materials/adding-additional-compression-filters-to-rhdf5 Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Mike Smith

New RNA-seq workflows

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: RNAseq

New RNA-seq workflows https://bioconductor.org2016/CSAMA/lect-07-modern-rnaseq/ModernRNAseqAnalysis.pdf https://tess.elixir-europe.org/materials/new-rna-seq-workflows Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Charlotte Soneson RNAseq

04: Practical: Organizing data with SummarizedExperiment

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Intro

04: Practical: Organizing data with SummarizedExperiment https://bioconductor.org/help/course-materials/2019/BSS2019/04_Practical_CoreApproachesInBioconductor.html https://tess.elixir-europe.org/materials/04-practical-organizing-data-with-summarizedexperiment Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan Intro

Low-level exploratory data analysis and methods development for RNA-seq

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Scientific topics: RNA-Seq

Low-level exploratory data analysis and methods development for RNA-seq https://bioconductor.org2016/BioC2016/ConcurrentWorkshops3/Love/bioc2016eda.html https://tess.elixir-europe.org/materials/low-level-exploratory-data-analysis-and-methods-development-for-rna-seq Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Michael Love RNA-Seq

Annotations

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Annotations https://bioconductor.org2014/SeattleFeb2014/Annotation_slides.pdf https://tess.elixir-europe.org/materials/annotations Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Discussion: Guidelines for submitting data to ExperimentHub

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Discussion: Guidelines for submitting data to ExperimentHub https://bioconductor.org/help/course-materials/2019/BiocDevelForum/03-ExperimentHub.pdf https://tess.elixir-europe.org/materials/discussion-guidelines-for-submitting-data-to-experimenthub Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Stephanie Hicks

Quantifying and lightening the package dependency burden

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Quantifying and lightening the package dependency burden https://bioconductor.org2020/BiocDevelForum/07-DependencyBurden.pdf https://tess.elixir-europe.org/materials/quantifying-and-lightening-the-package-dependency-burden Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Robert Castelo

Update: Bioconductor Images

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Update: Bioconductor Images https://bioconductor.org2020/BiocDevelForum/07-BiocDocker.pdf https://tess.elixir-europe.org/materials/update-bioconductor-images Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Nitesh Turaga

Windows and Rtools 4.0

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Windows and Rtools 4.0 https://bioconductor.org2020/BiocDevelForum/06-WinRtools.pdf https://tess.elixir-europe.org/materials/windows-and-rtools-4-0 Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Mike Smith

Continuous integration with Github Actions

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Continuous integration with Github Actions https://bioconductor.orghttps://github.com/seandavi/BuildABiocWorkshop2020 https://tess.elixir-europe.org/materials/continuous-integration-with-github-actions Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Sean Davis

Bioconductor updates and directions

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Bioconductor updates and directions https://bioconductor.orghttps://docs.google.com/presentation/d/e/2PACX-1vRgr1fiEBDWy548sMaa6SvK8WLPpayGGxDh7SNgstocTFC44LUyNo7mXrS1Fte4UkARaBVosNBQi4lN/pub https://tess.elixir-europe.org/materials/bioconductor-updates-and-directions Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Martin Morgan

Release schedule discussion

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Release schedule discussion https://bioconductor.org2021/BiocDevelForum/21-Release.mp4 https://tess.elixir-europe.org/materials/release-schedule-discussion Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Various

Updates to default caching location

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Updates to default caching location https://bioconductor.org2021/BiocDevelForum/21-Caching.pdf https://tess.elixir-europe.org/materials/updates-to-default-caching-location Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Lori Shepherd

Benchmarking out-of-memory strategies

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Performance

Benchmarking out-of-memory strategies https://bioconductor.org2016/CSAMA/lect-19-big-data/out-of-mem.pdf https://tess.elixir-europe.org/materials/benchmarking-out-of-memory-strategies Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Vincent J. Carey Performance

Q&A about upcoming release

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Q&A about upcoming release https://bioconductor.org2020/BiocDevelForum/14-release.mp4 https://tess.elixir-europe.org/materials/q-a-about-upcoming-release Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Lori Shepherd

Bioc vs. CRAN build systems

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Resource type: Talk

Bioc vs. CRAN build systems https://bioconductor.org2020/BiocDevelForum/08-buildsystems.mp4 https://tess.elixir-europe.org/materials/bioc-vs-cran-build-systems Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Various

Type