Files in waldronlab/subtypeHeterogeneity
Tumor subclonality of expression-based cancer subtypes
.github/workflows/basic_checks.yaml
.gitignore
DESCRIPTION
Dockerfile
NAMESPACE
R/analyze_subtype_clonality.R
R/population_ranges.R
R/scRNAseq.R
R/setup_subtype_clonality.R
R/tenx.R
R/viz_subtype_clonality.R
README.md
_pkgdown.yml
inst/extdata/ABSOLUTE_OV_grangeslist.rds
inst/extdata/ABSOLUTE_OV_grangeslist_hg38.rds
inst/extdata/ABSOLUTE_Purity_Ploidy.rds
inst/extdata/ABSOLUTE_Purity_Ploidy.txt.bz2
inst/extdata/ABSOLUTE_grangeslist.rds
inst/extdata/FT_vs_OSE_signature.txt
inst/extdata/GSE101108_consensus_subtypes.rds
inst/extdata/GSE101108_metadata_histotype.txt
inst/extdata/MetaGxOvarian_consensus_subtypes.rds
inst/extdata/PureCN_OV_S0293689_grangeslist.rds
inst/extdata/PureCN_Purity_Ploidy.txt
inst/extdata/PureCN_Purity_Ploidy_new.txt
inst/extdata/T59_cyclone.rds
inst/extdata/T77_cyclone.rds
inst/extdata/T90_cyclone.rds
inst/extdata/TCGA_mastercalls.abs_segtabs.fixed.txt.bz2
inst/extdata/Verhaak_100genes.txt
inst/extdata/Verhaak_supplementT8A.txt
inst/extdata/all_cancer_types.rds
inst/extdata/bulk_cpm_subtypes.rds
inst/extdata/bulk_raw_subtypes.rds
inst/extdata/consensus_subtypes_TCGA_marray_huex.rds
inst/extdata/consensus_subtypes_downsampled_tcgabulk_rseq.rds
inst/extdata/consensus_subtypes_verhaak100.rds
inst/extdata/consensus_subtypes_verhaak100_logTPMgr3.rds
inst/extdata/consensus_subtypes_verhaak800.rds
inst/extdata/consensus_subtypes_verhaak800_logTPMgr3.rds
inst/extdata/cytoBand_hg19.txt
inst/extdata/esets.rescaled.classified.filtered.RData
inst/extdata/gisticOV_ranges_hg19.txt
inst/extdata/gisticOV_ranges_hg38.txt
inst/extdata/hg19ToHg38.over.chain
inst/extdata/ovc_cnv_genes.txt
inst/extdata/pooled_subtypes.rds
inst/extdata/scRNAseq_celltypes.txt
inst/extdata/scRNAseq_consensusOV_genes.txt
inst/extdata/scRNAseq_symbols.rds
inst/extdata/scRNAseq_verhaak800.txt
inst/scripts/ccycle.R
inst/scripts/cnsigs.R
inst/scripts/extract_pureCN_granges.R
inst/scripts/ggplot_figures.R
inst/scripts/infercnv.R
inst/scripts/infercnv_results.R
inst/scripts/monocle2.R
inst/scripts/monocle3.R
inst/scripts/plotly_figures.R
inst/scripts/process_IGC.R
inst/scripts/run_scater.Rmd
inst/scripts/sc_annotate.R
inst/scripts/sc_cluster.R
inst/scripts/sc_preproc.R
inst/scripts/singleR.R
inst/scripts/slingshot.R
inst/scripts/tenx_bulk.R
inst/scripts/tenx_scRNAseq.R
vignettes/singlecell.Rmd
vignettes/subtypeHeterogeneity.Rmd
