Summary and Setup

RNA sequencing (RNA-seq) has revolutionized the field of genomics, enabling researchers to gain insights into gene expression, transcriptome dynamics, and molecular pathways. Bioconductor is an open-source software project that provides a rich set of tools for analyzing high-throughput genomic data, including RNA-seq data. This Carpentries-style workshop is designed to equip participants with the essential skills and knowledge needed to analyze RNA-seq data using the Bioconductor ecosystem. Throughout this workshop, you will delve into key concepts, including data preprocessing, quality control, differential gene expression analysis, visualization of results, and gene set analysis.

Callout

This workshop has been adapted from the original RNA-seq analysis with Bioconductor and customised for delivery on NeSI as part of the Otago Bioinformatics Spring School

Prerequisites

Familiarity with R/Bioconductor, such as the Introduction to data analysis with R and Bioconductor lesson.
Familiarity with statistical hypothesis testing, such as Chapter 6 of Modern Statistics for Modern Biology book by Holmes and Huber.
Familiarity with the biology of gene expression and RNA-seq, such as RNA sequencing: the teenage years manuscript by Hadfield et.al.

Ensure that you have the most recent versions of R and RStudio installed on your computer. For detailed instructions on how to do this, you can refer to the section “If you already have R and RStudio installed” in the Introduction to R episode of the Introduction to data analysis with R and Bioconductor lesson.

Additionally, you will also need to install the following packages that will be used throughout the lesson.

R

install.packages(c("BiocManager", "remotes"))
BiocManager::install(c("tidyverse", "SummarizedExperiment",
                       "ExploreModelMatrix", "AnnotationDbi", "org.Hs.eg.db", 
                       "org.Mm.eg.db", "csoneson/ConfoundingExplorer",
                       "DESeq2", "vsn", "ComplexHeatmap", "hgu95av2.db",
                       "RColorBrewer", "hexbin", "cowplot", "iSEE",
                       "clusterProfiler", "enrichplot", "kableExtra",
                       "msigdbr", "gplots", "ggplot2", "simplifyEnrichment",
                       "apeglm", "microbenchmark", "Biostrings",
                       "SingleCellExperiment"))

If you are attending a workshop, please complete all of the above before the workshop. Should you need help, an instructor will be available 30 minutes before the workshop commences to assist.