Man pages for FunGeST/Palimpsest
Package
| add_DBS_cats_ToVCF | add_DBS_cats_ToVCF |
| add_ID_cats_ToVCF | add_ID_cats_ToVCF |
| annotate_VCF | annotate_VCF |
| bed2index | bed2index |
| chrTime_annot | chrTime_annot |
| chrTime_plot | chrTime_plot |
| cit.chromString2num | cit.chromString2num |
| cit.density | cit.density |
| cit.discretize | cit.discretize |
| cit.genomOrder | cit.genomOrder |
| cit.pangenomCoord | cit.pangenomCoord |
| cit.pangenomPlot | cit.pangenomPlot |
| cit.peaks | cit.peaks |
| cnaCCF_annot | cnaCCF_annot |
| cnaCCF_plots | cnaCCF_plots |
| compare_results | compare_results |
| count_triplets | count_triplets |
| deconvolution_compare | deconvolution_compare |
| deconvolution_exposure | deconvolution_exposure |
| deconvolution_fit | deconvolution_fit |
| deconvolution_fit_SV | deconvolution_fit_SV |
| extract_dbs_from_vcf | extract_dbs_from_vcf |
| factoall | factoall |
| factochar | factochar |
| generate_table | generate_table |
| grapes-not-in-grapes | "Not in" function |
| indel_category_correct | indel_category_correct |
| load2object | load2object |
| makeMutypeMatFromVcf | makeMutypeMatFromVcf |
| make_plot | make_plot |
| NMF_Extraction | NMF_Extraction |
| order_vcf | order_vcf |
| palimpsest_addMutationContextToVR | palimpsest_addMutationContextToVR |
| palimpsest_addSVcategoriesToVcf | palimpsest_addSVcategoriesToVcf |
| palimpsest_CCFplot | palimpsest_CCFplot |
| palimpsest_clonalitySigsCompare | palimpsest_clonalitySigsCompare |
| palimpsest_cnvProfile | palimpsest_cnvProfile |
| palimpsest_dfPosXSegm | palimpsest_dfPosXSegm |
| palimpsest_dfPosXSegm_2 | palimpsest_dfPosXSegm_2 |
| palimpsest_DissectSigs | palimpsest_DissectSigs |
| palimpsest_distCosine | palimpsest_distCosine |
| palimpsest_Fireworks | palimpsest_Fireworks |
| palimpsest_input | palimpsest_input |
| palimpsest_makeMutypeMatFromVcf | palimpsest_makeMutypeMatFromVcf |
| palimpsest_plotTumorHistories | palimpsest_plotTumorHistories |
| plot6mutationSpectrumFromVcf | plot6mutationSpectrumFromVcf |
| plot96mutationSpectrumFromVcf | plot96mutationSpectrumFromVcf |
| plot_signatures | plot_signatures |
| plotStrandBias6types | plotStrandBias6types |
| plotStrandBias96types | plotStrandBias96types |
| plotSubstypeNumberPerSample | plotSubstypeNumberPerSample |
| plot.SV.sigs | plot.SV.sigs |
| preprocessInput_sv | preprocessInput_sv |
| rainfallz_plot | rainfallz_plot |
| RCircos.Get.Start.End.Locations_1 | RCircos.Get.Start.End.Locations_1 |
| RCircos.Heatmap.Plot_1 | RCircos.Heatmap.Plot_1 |
| RCircos.Link.Plot_1 | RCircos.Link.Plot_1 |
| signature_colour_generator | signature_colour_generator |
| signature_exposure_plot | signature_exposure_plot |
| signature_origins | signature_origins |
