RNA-seq pipeline in R/Bash enables QC, alignment, read counting, and differential expression using Bioconductor; reproducible workflow on Ubuntu with Conda. 🐙

In total there are 3 jupyter notebooks together with 3 html files for ease of access in this repository. (1) Master notebook & FastQC and Mapping of reads using star and subsequent feature count (this notebook), (2) the DESeq2 analysis in R for the statistical analysis, (3) Functional analysis using arbitrary (GProfiler, iRegulon) and "leading e…