Exercises for transcriptome analysis workshop taught at UNAM-Morelia, Mexico in January 2019. Topics include Linux basics, Illumina data quality assessment, quantifying gene expression levels with RNA-Seq, testing for differential expression among experimental treatments, and weighted gene coexpression network analysis.
Windows: PuTTY and FTP client (e.g., FileZilla or WinSCP)
MacOs: FTP client (e.g., FileZilla)
fastqc (see "Requirements" section for dependencies)
Then in R, run the following commands to install necessary packages (and any dependencies):
install.packages(c("gplots", "pheatmap", "RColorBrewer", "igraph"))
if (!requireNamespace("BiocManager"))
install.packages("BiocManager")
BiocManager::install()
BiocManager::install(c("qvalue", "DESeq2", "WGCNA", "Rsubread", "genefilter"))