Github repo for AIH data analysis.
For more information, please refer to this paper: Tana MM-S, Klepper A, Lyden A, Pisco AO, Phelps M, McGee B, et al. (2022) Transcriptomic profiling of blood from autoimmune hepatitis patients reveals potential mechanisms with implications for management. PLoS ONE 17(3): e0264307.
AIH-metadata include R scripts for reformatting metadata
AIH-PriceSeqFilter includes scripts, presentations and figures for analyzing effects of various PriceSeqFilter parameters and cutadapt on differential gene expression analysis
DifferentialGeneExpression-R-Scripts includes DESeq2, EdgeR, WGCNA and various plotting scripts (ie PCA, MA etc) for AIH differential gene expression analysis
DifferentialGeneExpression-Output includes figures, CSVs and Excel tables produced which display differential gene expression analysis, and can be used for IPA analysis.
IPA-Summary-Analyses-Export contains files exported from the pathway analysis software IPA.
Pegivirus-Analysis contains scripts and figures related to phylogeny of pegivirus in our samples