Files in HuntsmanCancerInstitute/hciR
RNA-seq workflows at HCI
.Rbuildignore
.gitignore
ChangeLog
DESCRIPTION
NAMESPACE
R/annotate_results.R
R/as_matrix.R
R/check_contrasts.R
R/data.R
R/deseq_from_tibble.R
R/extract_samples.R
R/fgsea_all.R
R/filter_counts.R
R/filter_top_counts.R
R/gdc_coldata.R
R/gdc_rowdata.R
R/gene_intersect.R
R/globalVar.R
R/palette255.R
R/pipe.R
R/plot_biotypes.R
R/plot_counts.R
R/plot_dist.R
R/plot_fgsea.R
R/plot_filter.R
R/plot_genes.R
R/plot_interactions.R
R/plot_ma.R
R/plot_pca.R
R/plot_volcano.R
R/print_genes.R
R/r_log.R
R/read_RSEM.R
R/read_RnaSeqMetrics.R
R/read_STAR.R
R/read_biomart.R
R/read_deseq.R
R/read_featureCounts.R
R/read_gsea.R
R/read_idxstats.R
R/read_ipa.R
R/read_sample_files.R
R/results2.R
R/results_all.R
R/results_apeglm.R
R/sort_counts.R
R/sort_samples.R
R/summary_DESeq.R
R/summary_tibble.R
R/top_counts.R
R/top_genes.R
R/write_deseq.R
R/write_gsea_rnk.R
R/write_ipa.R
README.md
data/pasilla.rda
docs/TCGA.html
docs/pasilla_flex.html
docs/volcano.html
inst/extdata/liver_counts.tsv
inst/extdata/liver_samples.tsv
inst/extdata/pasilla_counts.tsv
inst/extdata/pasilla_samples.tsv
man/annotate_results.Rd
man/as_matrix.Rd
man/check_contrasts.Rd
man/deseq_from_tibble.Rd
man/extract_samples.Rd
man/fgsea_all.Rd
man/filter_counts.Rd
man/filter_top_counts.Rd
man/gdc_coldata.Rd
man/gdc_rowdata.Rd
man/gene_intersect.Rd
man/palette255.Rd
man/pasilla.Rd
man/plot_biotypes.Rd
man/plot_counts.Rd
man/plot_dist.Rd
man/plot_fgsea.Rd
man/plot_filter.Rd
man/plot_genes.Rd
man/plot_interactions.Rd
man/plot_ma.Rd
man/plot_pca.Rd
man/plot_volcano.Rd
man/print_genes.Rd
man/r_log.Rd
man/read_RSEM.Rd
man/read_RnaSeqMetrics.Rd
man/read_STAR.Rd
man/read_biomart.Rd
man/read_deseq.Rd
man/read_featureCounts.Rd
man/read_gsea.Rd
man/read_idxstats.Rd
man/read_ipa.Rd
man/read_sample_files.Rd
man/reexports.Rd
man/results2.Rd
man/results_all.Rd
man/results_apeglm.Rd
man/sort_counts.Rd
man/sort_samples.Rd
man/summary_deseq.Rd
man/summary_tibble.Rd
man/top_counts.Rd
man/top_genes.Rd
man/write_deseq.Rd
man/write_gsea_rnk.Rd
man/write_ipa.Rd
vignettes/Ensembl.Rmd
vignettes/Ensembl.md
vignettes/Liver.Rmd
vignettes/Liver.md
vignettes/Liver_files/figure-gfm/dist-1.png
vignettes/Liver_files/figure-gfm/enrich1-1.png
vignettes/Liver_files/figure-gfm/enrich2-1.png
vignettes/Liver_files/figure-gfm/gene_heatmap1-1.png
vignettes/Liver_files/figure-gfm/gene_heatmap2-1.png
vignettes/Liver_files/figure-gfm/gene_heatmap2b-1.png
vignettes/Liver_files/figure-gfm/gene_heatmap3-1.png
vignettes/Liver_files/figure-gfm/interactionPlot-1.png
vignettes/Liver_files/figure-gfm/pcaplot-1.png
vignettes/Liver_files/figure-gfm/plot_ma1-1.png
vignettes/Liver_files/figure-gfm/plotfgsea-1.png
vignettes/Liver_files/figure-gfm/volcano-1.png
vignettes/Pasilla.Rmd
vignettes/Pasilla.md
vignettes/Pasilla_files/figure-gfm/dist-1.png
vignettes/Pasilla_files/figure-gfm/gene_heatmap1c-1.png
vignettes/Pasilla_files/figure-gfm/pcaplot-1.png
vignettes/Pasilla_files/figure-gfm/plot1-1.png
vignettes/Pasilla_files/figure-gfm/plot_filter-1.png
vignettes/Pasilla_files/figure-gfm/volcano-1.png
