Introduction

This page holds the resources for the two workshops I facilitate on the use of R and RStudio for bioinformatics, focusing on their use for differential expression analysis of Illumina HTS RNA-seq data using the Rsubread and edgeR packages. There is more material and resources on this site than is presented in the workshops, but some of this will serve as background and extended reading/activities for the interested.

Workshop 1

Part 1: RStudio

Quick Introduction to R RStudio and Rmarkdown for reproducible research a short Powerpoint presentation on the tools R provides for generating reproducible reseach documentation of your bioinformatics analysis, and a hands-on workshop using the Compbio RStudio Server.

• the powerpoint slide are here
• the activities are here
• the code for the activities page is here

Part 2: Bioconductor

Introduction to the features of Bioconductor, a library of packages for R for processing biological data. Inparticular in introduction to 3 packages Biostrings, GenomicRanges and GenomicAlignments that for a core set of classes on which many other bioconductor packages draw. Depending on time available there are workshop activities to explore some of the features of these packages.

• the powerpoint slide are here
• the activities are here
• the code for the activities page is here

Part 3: RNA-seq

An overview of RNA-seq and aspects of library preparation that have an impact upon downstream analysis, and the special features of RNA-seq reads as compared to ChIP-seq reads, that affect the choices for alignment and feature mapping quantification.

• powerpoint slides

Part :4 R NGS

Introduction to R/Bioconductor for NGS processing introduces the Rsubread package. A package for aligning short read RNA-seq and ChIP-seq data to a reference.

• the activities are here
• the code of the activities is here

Workshop 2

Part 1: DGE with edgeR

Introduction to the statistics of differential gene expression and a workshop on the use of the edgeR package for performing DGE analysis

• powerpoint slides
• the activities are here
• the code of the activities is here

Part 2: Functional Annotation

Introduction functional annotation via the STRINGdb package one of many bioconductor packages for examining the functional annotation enrichment in set of genes called significant by differential expression.

• the activities are here
• the code of the activities is here

Resources

Data Files

There are some data files used in the exercises that are available on the teaching server they are also downloadable from here

PowerPoints and PDFs

Powerpoints of the lectures and PDF’s of the workshops can be downloaded from here