Register training material
12 materials found

Authors: Jenny Drnevich @jenny 


Introduction to R and Bioconductor lecture

This reference handout goes over how to read and parse a line of complex R code.

Keywords: R-programming

Introduction to R and Bioconductor lecture https://tess.elixir-europe.org/materials/introduction-to-r-and-bioconductor-lecture-990e00de-2241-49f5-9577-5c110cc06a64 This reference handout goes over how to read and parse a line of complex R code. R-programming
Guide to R swirl interactive lessons

This handout describes how to download the swirl package and start the basic interactive lessons to learn R.

Keywords: R-programming

Guide to R swirl interactive lessons https://tess.elixir-europe.org/materials/guide-to-r-swirl-interactive-lessons This handout describes how to download the swirl package and start the basic interactive lessons to learn R. R-programming
Day 4 - RNA-Seq Analysis

Day 4 focuses on the final steps after production of significant gene lists, including gene clustering, visualization, and annotation.

Keywords: Exploratory-analysis, Differential-expression, Statistical-model, Annotation

Day 4 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-4-rna-seq-analysis Day 4 focuses on the final steps after production of significant gene lists, including gene clustering, visualization, and annotation. Exploratory-analysis, Differential-expression, Statistical-model, Annotation
Introduction to R practice codes

These codes give an overview of R object types and programming language structure.

Keywords: R-programming

Introduction to R practice codes https://tess.elixir-europe.org/materials/introduction-to-r-practice-codes These codes give an overview of R object types and programming language structure. R-programming
R/Bioconductor installation and upgrade guide

This handout describes how to download R and install add-on packages, both from CRAN and

Keywords: R-programming

R/Bioconductor installation and upgrade guide https://tess.elixir-europe.org/materials/r-bioconductor-installation-and-upgrade-guide This handout describes how to download R and install add-on packages, both from CRAN and R-programming
Day 3 - RNA-Seq Analysis

Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons.

Keywords: QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing

Day 3 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-3-rna-seq-analysis Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons. QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing
Intro to R and Bioconductor

R is a free, open-source software environment and programming language for statistical computing and graphics. It is available for all computer platforms and is widely used, and many packages have been developed in the Bioconductor project for analysis of genomic data. This module covers the...

Keywords: Prerequisite, R-programming

Intro to R and Bioconductor https://tess.elixir-europe.org/materials/intro-to-r-and-bioconductor R is a free, open-source software environment and programming language for statistical computing and graphics. It is available for all computer platforms and is widely used, and many packages have been developed in the Bioconductor project for analysis of genomic data. This module covers the basic skills that will be needed before using R to analyze NGS data. Prerequisite, R-programming
RNA-Seq Analysis with Biocluster and R

Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model

RNA-Seq Analysis with Biocluster and R https://tess.elixir-europe.org/materials/rna-seq-analysis-with-biocluster-and-r Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it RNA-Seq RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model
Introduction to R and Bioconductor lecture

This lecture gives an overview of the R and Bioconductor projects, plus the basics of R object types and programming language structure.

Keywords: R-programming

Introduction to R and Bioconductor lecture https://tess.elixir-europe.org/materials/introduction-to-r-and-bioconductor-lecture This lecture gives an overview of the R and Bioconductor projects, plus the basics of R object types and programming language structure. R-programming
Day 1 - RNA-Seq Analysis

Day 1 starts at the very beginning of a typical RNA-Seq workflow, explaining the sequencing technology and considerations for experimental design, then starts with hands-on application of working with sequencing data fresh off the sequencer.

Keywords: Alignment, BAM, FASTA, FASTQ, QC

Day 1 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-1-rna-seq-analysis Day 1 starts at the very beginning of a typical RNA-Seq workflow, explaining the sequencing technology and considerations for experimental design, then starts with hands-on application of working with sequencing data fresh off the sequencer. Alignment, BAM, FASTA, FASTQ, QC
Data objects for R practice codes

This RData file contains small R objects to use in the [introR.R practice questions](introR.R)

Keywords: R-programming

Data objects for R practice codes https://tess.elixir-europe.org/materials/data-objects-for-r-practice-codes This RData file contains small R objects to use in the [introR.R practice questions](introR.R) R-programming
Day 2 - RNA-Seq Analysis

Day 2 continues throught the steps in a typical RNA-Seq experiment from alignment to sample QC and count normalization, including a brief overview of the IGV Genome Browser.

Keywords: Alignment, BAM, FASTA, FASTQ, QC, Exploratory-analysis, Feature-summarisation, Pre-processing

Day 2 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-2-rna-seq-analysis Day 2 continues throught the steps in a typical RNA-Seq experiment from alignment to sample QC and count normalization, including a brief overview of the IGV Genome Browser. Alignment, BAM, FASTA, FASTQ, QC, Exploratory-analysis, Feature-summarisation, Pre-processing