This repo contains code used to obtain results and figures in the article Valyaeva AA, Tikhomirova MA, Potashnikova DM, Bogomazova AN, Snigiryova GP, Penin AA, Logacheva MD, Arifulin EA, Shmakova AA, Germini D, Kachalova AI, Saidova AA, Zharikova AA, Musinova YR, Mironov AA, Vassetzky YS, Sheval EV. 2022. Ectopic expression of HIV-1 Tat modifies gene expression in cultured B cells: implications for the development of B-cell lymphomas in HIV-1-infected patients. PeerJ 10:e13986 https://doi.org/10.7717/peerj.13986.
The raw and processed RNA-seq data (fastq files and gene counts) are deposited in GEO with accession number GSE182538.
Note: because of multiple possible conflicts between different R packages (e.g. dplyr and clusterProfiler) try running each script in separate R sessions.