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

waldronlab/subtypeHeterogeneity documentation built on Oct. 28, 2020, 9:14 a.m.