- BioCartaImage::BC2ENTREZPre-computed data objects
- BioCartaImage::BIOCARTA_PATHWAYSPre-computed data objects
- BioCartaImage::PATHWAY2BCPre-computed data objects
- BioCartaImage::PATHWAY2ENTREZPre-computed data objects
- BioCartaImage::PATHWAY2MSIGDBPre-computed data objects
- CePa::PID.dbpathway catalogues from Pathway Interaction Database(PID)
- CePa::gene.listDifferential gene list and background gene list
- cola::cola_rlExample ConsensusPartitionList object
- cola::golub_colaExample ConsensusPartitionList object from Golub dataset
- cola::golub_cola_dsExample DownSamplingConsensusPartition object from Golub dataset
- cola::golub_cola_rhExample HierarchicalPartition object from Golub dataset
- InteractiveComplexHeatmap::rand_matA random matrix
- YAPSA::AlexCosmicArtif_sigInd_dfData for mutational signatures
- YAPSA::AlexCosmicArtif_sig_dfData for mutational signatures
- YAPSA::AlexCosmicValid_sigInd_dfData for mutational signatures
- YAPSA::AlexCosmicValid_sig_dfData for mutational signatures
- YAPSA::AlexCosmicValid_sig_dfData for mutational signatures
- YAPSA::AlexInitialArtif_sigInd_dfData for mutational signatures
- YAPSA::AlexInitialArtif_sig_dfData for mutational signatures
- YAPSA::AlexInitialValid_sigInd_dfData for mutational signatures
- YAPSA::AlexInitialValid_sig_dfData for mutational signatures
- YAPSA::COSMIC_subgroups_dfTest and example data
- YAPSA::GenomeOfNl_rawExample data for the Indel vignette
- YAPSA::MutCat_indel_dfExample mutational catalog for the Indel vignette
- YAPSA::PCAWG_SP_ID_sigInd_dfData for PCAWG SNV signatures (COSMIC v3), including artifacts 'PCAWG_SP_SBS_sigs_Artif_df': Data frame of the signatures published by Alexandrov et al. (Biorxiv 2013) which were decomposed with the method SigProfiler. SNV signatures are labeled with SBS, single base signature. There are 67 signatures which constitute the columns, 47 of which were validated by a bayesian NFM mehtod, SignatureAnayzer. Validated signatures are SBS1-SBS26,SBS28-SBS42 and SBS44. SBS7 is split up into 7 a/b/c and d. SBS10 ans SBS17 are both split up into a and b. Resulting in a 47 validated sigantures. Please note, unlike the paper by Alexandrov et al. (Biorxiv 2018) the data sets do not contain a SBS84 and SBS85 as not all were availiablt to perfom supervised signature analysis. In total there are 96 different features and therefore 96 rows when dealing with a trinucleotide context.
- YAPSA::PCAWG_SP_ID_sigs_dfData for PCAWG SNV signatures (COSMIC v3), including artifacts 'PCAWG_SP_SBS_sigs_Artif_df': Data frame of the signatures published by Alexandrov et al. (Biorxiv 2013) which were decomposed with the method SigProfiler. SNV signatures are labeled with SBS, single base signature. There are 67 signatures which constitute the columns, 47 of which were validated by a bayesian NFM mehtod, SignatureAnayzer. Validated signatures are SBS1-SBS26,SBS28-SBS42 and SBS44. SBS7 is split up into 7 a/b/c and d. SBS10 ans SBS17 are both split up into a and b. Resulting in a 47 validated sigantures. Please note, unlike the paper by Alexandrov et al. (Biorxiv 2018) the data sets do not contain a SBS84 and SBS85 as not all were availiablt to perfom supervised signature analysis. In total there are 96 different features and therefore 96 rows when dealing with a trinucleotide context.
- YAPSA::PCAWG_SP_SBS_sigInd_Artif_dfData for PCAWG SNV signatures (COSMIC v3), including artifacts 'PCAWG_SP_SBS_sigs_Artif_df': Data frame of the signatures published by Alexandrov et al. (Biorxiv 2013) which were decomposed with the method SigProfiler. SNV signatures are labeled with SBS, single base signature. There are 67 signatures which constitute the columns, 47 of which were validated by a bayesian NFM mehtod, SignatureAnayzer. Validated signatures are SBS1-SBS26,SBS28-SBS42 and SBS44. SBS7 is split up into 7 a/b/c and d. SBS10 ans SBS17 are both split up into a and b. Resulting in a 47 validated sigantures. Please note, unlike the paper by Alexandrov et al. (Biorxiv 2018) the data sets do not contain a SBS84 and SBS85 as not all were availiablt to perfom supervised signature analysis. In total there are 96 different features and therefore 96 rows when dealing with a trinucleotide context.
- YAPSA::PCAWG_SP_SBS_sigInd_Real_dfData for PCAWG SNV signatures (COSMIC v3), including artifacts 'PCAWG_SP_SBS_sigs_Artif_df': Data frame of the signatures published by Alexandrov et al. (Biorxiv 2013) which were decomposed with the method SigProfiler. SNV signatures are labeled with SBS, single base signature. There are 67 signatures which constitute the columns, 47 of which were validated by a bayesian NFM mehtod, SignatureAnayzer. Validated signatures are SBS1-SBS26,SBS28-SBS42 and SBS44. SBS7 is split up into 7 a/b/c and d. SBS10 ans SBS17 are both split up into a and b. Resulting in a 47 validated sigantures. Please note, unlike the paper by Alexandrov et al. (Biorxiv 2018) the data sets do not contain a SBS84 and SBS85 as not all were availiablt to perfom supervised signature analysis. In total there are 96 different features and therefore 96 rows when dealing with a trinucleotide context.
- YAPSA::PCAWG_SP_SBS_sigs_Artif_dfData for PCAWG SNV signatures (COSMIC v3), including artifacts 'PCAWG_SP_SBS_sigs_Artif_df': Data frame of the signatures published by Alexandrov et al. (Biorxiv 2013) which were decomposed with the method SigProfiler. SNV signatures are labeled with SBS, single base signature. There are 67 signatures which constitute the columns, 47 of which were validated by a bayesian NFM mehtod, SignatureAnayzer. Validated signatures are SBS1-SBS26,SBS28-SBS42 and SBS44. SBS7 is split up into 7 a/b/c and d. SBS10 ans SBS17 are both split up into a and b. Resulting in a 47 validated sigantures. Please note, unlike the paper by Alexandrov et al. (Biorxiv 2018) the data sets do not contain a SBS84 and SBS85 as not all were availiablt to perfom supervised signature analysis. In total there are 96 different features and therefore 96 rows when dealing with a trinucleotide context.
- YAPSA::PCAWG_SP_SBS_sigs_Real_dfData for PCAWG SNV signatures (COSMIC v3), including artifacts 'PCAWG_SP_SBS_sigs_Artif_df': Data frame of the signatures published by Alexandrov et al. (Biorxiv 2013) which were decomposed with the method SigProfiler. SNV signatures are labeled with SBS, single base signature. There are 67 signatures which constitute the columns, 47 of which were validated by a bayesian NFM mehtod, SignatureAnayzer. Validated signatures are SBS1-SBS26,SBS28-SBS42 and SBS44. SBS7 is split up into 7 a/b/c and d. SBS10 ans SBS17 are both split up into a and b. Resulting in a 47 validated sigantures. Please note, unlike the paper by Alexandrov et al. (Biorxiv 2018) the data sets do not contain a SBS84 and SBS85 as not all were availiablt to perfom supervised signature analysis. In total there are 96 different features and therefore 96 rows when dealing with a trinucleotide context.
- YAPSA::chosen_signatures_indices_dfTest and example data
- YAPSA::cutoffCosmicArtif_abs_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffCosmicArtif_rel_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffCosmicValid_abs_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffCosmicValid_rel_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffInitialArtif_abs_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffInitialArtif_rel_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffInitialValid_abs_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffInitialValid_rel_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffPCAWG_ID_WGS_Pid_dfOpt. cutoffs, PCAWG SNV signatures, including artifacts
- YAPSA::cutoffPCAWG_SBS_WGSWES_artifPid_dfOpt. cutoffs, PCAWG SNV signatures, including artifacts
- YAPSA::cutoffPCAWG_SBS_WGSWES_realPid_dfOpt. cutoffs, PCAWG SNV signatures, including artifacts
- YAPSA::exchange_colour_vectorColours codes for displaying SNVs
- YAPSA::exome_mutCatRaw_dfExample mutational catalog for the exome vignette
- YAPSA::lymphomaNature2013_mutCat_dfExample mutational catalog for the SNV vignette
- YAPSA::lymphoma_Nature2013_COSMIC_cutoff_exposures_dfTest and example data
- YAPSA::lymphoma_Nature2013_raw_dfTest and example data
- YAPSA::lymphoma_PID_dfTest and example data
- YAPSA::lymphoma_test_dfTest and example data
- YAPSA::rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_dfTest and example data
- YAPSA::targetCapture_cor_factorsCorrection factors for different target capture kits
