katagirya/differential-transcript-expression-analysis: CAfGEN DET analysis

This release provides the set of scripts used for RNA-seq data processing and downstream analysis described in the manuscript "Conserved neutrophil degranulation transcripts in HIV–TB coinfected children across East and Southern Africa." The repository includes scripts for: FASTQ quality control of raw RNA-seq data Transcript quantification using Salmon Differential expression analysis using DESeq2 Construction of protein–protein interaction (PPI) networks These analyses were performed on bulk RNA-seq data from children living with HIV in Uganda, Botswana, and Eswatini as part of the CAfGEN consortium study.