SexChrLab / Viral_HCC_Sex_Diff

Viral_HCC_Sex_Diff

Last updated by: Elizabeth Borden

Contact: [e-mail]

Contents

All visualization and downstream analyses for the manuscript entitled "Unique Immune Landscapes in HCV and HBV-mediated Hepatocellular Carcinoma" are included here in Rmarkdown format.

Processing

• Code and results for initial FASTQ QC analysis

• Read mapping and read count quantification code

QC

• Analysis of sex and tumor status across all available samples

• Removal of samples not matching their sex or tumor status of origin (methods detailed in manuscript supplementary materials)

• Visualization and statistical analyses of potential covariates for differential expression analysis

DEA_Analyses

• Tumor vs. tumor-adjacent, subset by sex and etiology

• Tumor vs. tumor-adjacent, down-sampling of male samples

• HBV vs. HCV, subset by tumor and tumor-adjacent

Immune cell deconvolution

• All code for immune cell deconvolution analyses and visualization

Visualizations

• Volcano plots

• Upset plots

• LogFC plots

• Pathway analyses/Treemaps