Files in FunGeST/Palimpsest
Package
.DS_Store
DESCRIPTION
Files/.DS_Store
Files/Palimpsest.jpg
Files/RUNNING_PALIMPSEST.png
Files/vignette_palimpsest_2.0.pdf
NAMESPACE
Palimpsest.Rproj
R/SV_functions.R
R/annotate_VCF_functions.R
R/palimpsest_clonality.R
R/palimpsest_deconvolution.R
R/palimpsest_input.R
R/palimpsest_plotting.R
R/palimpsest_plotting_2.R
R/palimpsest_timings.R
R/palimpsest_utils.R
R/sysdata.rda
README.md
RUNNING_PALIMPSEST_EXAMPLE/.DS_Store
RUNNING_PALIMPSEST_EXAMPLE/LiC1162/annot_data.RData
RUNNING_PALIMPSEST_EXAMPLE/LiC1162/cna_data.RData
RUNNING_PALIMPSEST_EXAMPLE/LiC1162/sv_data.RData
RUNNING_PALIMPSEST_EXAMPLE/LiC1162/vcf.RData
RUNNING_PALIMPSEST_EXAMPLE/Palimpsest_Test_Script.R
data/DBS_colors.RData
data/DBS_cosmic.rda
data/ID_colors.RData
data/ID_cosmic.rda
data/Relevant_DBS_signatures_per_cancer_type_Alexandrov2020.RData
data/Relevant_DBS_signatures_per_cancer_type_Alexandrov2020.txt
data/Relevant_ID_signatures_per_cancer_type_Alexandrov2020.RData
data/Relevant_ID_signatures_per_cancer_type_Alexandrov2020.txt
data/Relevant_SBS_signatures_per_cancer_type_Alexandrov2020.RData
data/Relevant_SBS_signatures_per_cancer_type_Alexandrov2020.txt
data/SBS_COSMIC_v3.2.rda
data/SBS_colors.RData
data/SBS_cosmic.rda
data/UCSC.HG19.Human.CytoBandIdeogram.RData
data/UCSC.HG19.Human.CytoBandIdeogram.rda
data/cytoband_hg19.rda
data/cytoband_hg38.rda
data/ensgene_hg19.rda
data/ensgene_hg38.rda
data/sig_cols.rda
exec/.DS_Store
exec/GENCODE_transcripts.v19.hs37.bed
exec/GENCODE_transcripts.v20.grch38.bed
exec/README.txt
exec/get_reference.py
exec/get_reference.pyc
exec/gpl-license.txt
exec/in_target.py
exec/in_target.pyc
exec/lookups.pyc
exec/lookups_indels.py
exec/lookups_indels.pyc
exec/make_spectra_indels.py
man/.DS_Store
man/NMF_Extraction.Rd
man/RCircos.Get.Start.End.Locations_1.Rd
man/RCircos.Heatmap.Plot_1.Rd
man/RCircos.Link.Plot_1.Rd
man/add_DBS_cats_ToVCF.Rd
man/add_ID_cats_ToVCF.Rd
man/annotate_VCF.Rd
man/bed2index.Rd
man/chrTime_annot.Rd
man/chrTime_plot.Rd
man/cit.chromString2num.Rd
man/cit.density.Rd
man/cit.discretize.Rd
man/cit.genomOrder.Rd
man/cit.pangenomCoord.Rd
man/cit.pangenomPlot.Rd
man/cit.peaks.Rd
man/cnaCCF_annot.Rd
man/cnaCCF_plots.Rd
man/compare_results.Rd
man/count_triplets.Rd
man/deconvolution_compare.Rd
man/deconvolution_exposure.Rd
man/deconvolution_fit.Rd
man/deconvolution_fit_SV.Rd
man/extract_dbs_from_vcf.Rd
man/factoall.Rd
man/factochar.Rd
man/generate_table.Rd
man/grapes-not-in-grapes.Rd
man/indel_category_correct.Rd
man/load2object.Rd
man/makeMutypeMatFromVcf.Rd
man/make_plot.Rd
man/order_vcf.Rd
man/palimpsest_CCFplot.Rd
man/palimpsest_DissectSigs.Rd
man/palimpsest_Fireworks.Rd
man/palimpsest_addMutationContextToVR.Rd
man/palimpsest_addSVcategoriesToVcf.Rd
man/palimpsest_clonalitySigsCompare.Rd
man/palimpsest_cnvProfile.Rd
man/palimpsest_dfPosXSegm.Rd
man/palimpsest_dfPosXSegm_2.Rd
man/palimpsest_distCosine.Rd
man/palimpsest_input.Rd
man/palimpsest_makeMutypeMatFromVcf.Rd
man/palimpsest_plotTumorHistories.Rd
man/plot.SV.sigs.Rd
man/plot6mutationSpectrumFromVcf.Rd
man/plot96mutationSpectrumFromVcf.Rd
man/plotStrandBias6types.Rd
man/plotStrandBias96types.Rd
man/plotSubstypeNumberPerSample.Rd
man/plot_signatures.Rd
man/preprocessInput_sv.Rd
man/rainfallz_plot.Rd
man/signature_colour_generator.Rd
man/signature_exposure_plot.Rd
man/signature_origins.Rd
