Tag: RNA-seq

This post contains the analysis steps used to create a differential gene expression results table generated from RNA-seq counts summarised using nf-core/rnaseq. The comparison was done between two conditions: normal versus (lung) cancer. We will be using {edgeR}, so install it if you haven’t already. if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("edgeR") We will also…

A popular toolset used for analysing RNA-seq data is the tuxedo suite, which consists of TopHat and Cufflinks. The suite provided a start to finish pipeline that allowed users to map reads, assemble transcripts, and perform differential expression analyses. A newer “tuxedo suite” has been developed and is made up of three tools: HISAT, StringTie,…