TeSS Training eSupport System

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.org/help/course-materials/2014/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2017/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2017/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

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.org/help/course-materials/2016/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

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 / RNA-seq

R and Bioconductor for Genomic Analysis https://bioconductor.org/help/course-materials/2017/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 / RNA-seq

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/https://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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2014/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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2015/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

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/course-materials//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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2015/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 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.org/help/course-materials/2014/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2017/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/http://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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2017/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2014/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

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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/https://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

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.org/help/course-materials/https://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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2014/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 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.org/help/course-materials/2017/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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/course-materials//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

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.org/help/course-materials/2014/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

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.org/help/course-materials/http://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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2014/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

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.org/help/course-materials/2017/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

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.org/help/course-materials/2017/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

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.org/help/course-materials/2016/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

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.org/help/course-materials/2015/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

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.org/help/course-materials/2014/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

Type