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Viral_HCC_Sex_Diff

Last updated by: Elizabeth Borden

Contact: [email protected]

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