Last updated by: Elizabeth Borden
Contact: [email protected]
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
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Code and results for initial FASTQ QC analysis
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Read mapping and read count quantification code
QC
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Analysis of sex and tumor status across all available samples
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Removal of samples not matching their sex or tumor status of origin (methods detailed in manuscript supplementary materials)
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Visualization and statistical analyses of potential covariates for differential expression analysis
DEA_Analyses
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Tumor vs. tumor-adjacent, subset by sex and etiology
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Tumor vs. tumor-adjacent, down-sampling of male samples
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HBV vs. HCV, subset by tumor and tumor-adjacent
Immune cell deconvolution
- All code for immune cell deconvolution analyses and visualization
Visualizations
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Volcano plots
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Upset plots
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LogFC plots
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Pathway analyses/Treemaps