├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── aaa.R ├── assignSigPerMut.R ├── cosSim.R ├── dataDbsSignatureProfiles.R ├── dataIndelSignatureProfiles.R ├── dataSbsSignatureProfilesV2.R ├── dataSbsSignatureProfilesV3.R ├── dataSvSignatureProfiles.R ├── detHomology.R ├── extractSigsDbs.R ├── extractSigsIndel.R ├── extractSigsSnv.R ├── extractSigsSv.R ├── fitToSignatures.R ├── plotContexts.R ├── readSigsAsDf.R ├── readVcfFields.R ├── splitDfRegex.R ├── subsetSmnvs.R ├── transformContexts.R └── variantsFromVcf.R ├── README.md ├── data ├── DBS_SIGNATURE_PROFILES.RData ├── INDEL_SIGNATURE_PROFILES.RData ├── SBS_SIGNATURE_PROFILES_V2.RData ├── SBS_SIGNATURE_PROFILES_V3.RData ├── SV_SIGNATURE_PROFILES.RData └── raw │ ├── DBS-doublet-base-substitution-classification.xlsx │ ├── PCAWG7_indel_classification_2017_12_08.xlsx │ ├── indel_signatures │ ├── sigProfiler_ID_signatures_ID1.csv │ ├── sigProfiler_ID_signatures_ID10.csv │ ├── sigProfiler_ID_signatures_ID11.csv │ ├── sigProfiler_ID_signatures_ID12.csv │ ├── sigProfiler_ID_signatures_ID13.csv │ ├── sigProfiler_ID_signatures_ID14.csv │ ├── sigProfiler_ID_signatures_ID15.csv │ ├── sigProfiler_ID_signatures_ID16.csv │ ├── sigProfiler_ID_signatures_ID17.csv │ ├── sigProfiler_ID_signatures_ID18.csv │ ├── sigProfiler_ID_signatures_ID2.csv │ ├── sigProfiler_ID_signatures_ID3.csv │ ├── sigProfiler_ID_signatures_ID4.csv │ ├── sigProfiler_ID_signatures_ID5.csv │ ├── sigProfiler_ID_signatures_ID6.csv │ ├── sigProfiler_ID_signatures_ID7.csv │ ├── sigProfiler_ID_signatures_ID8.csv │ └── sigProfiler_ID_signatures_ID9.csv │ ├── sigProfiler_DBS_signatures.csv │ ├── sigProfiler_ID_signatures.csv │ ├── sigProfiler_ID_signatures_3.1.txt │ └── sigProfiler_SBS_signatures_2019_05_22.csv ├── doc ├── README.Rmd ├── README.md ├── extract_signatures.R └── vcf │ ├── COLO829v003T.purple.somatic.vcf.gz │ └── COLO829v003T.purple.sv.vcf.gz ├── inst └── sigs_v3.2_metadata.txt └── man ├── DBS_SIGNATURE_PROFILES.Rd ├── INDEL_SIGNATURE_PROFILES.Rd ├── SBS_SIGNATURE_PROFILES_V2.Rd ├── SBS_SIGNATURE_PROFILES_V3.Rd ├── SV_SIGNATURE_PROFILES.Rd ├── assignSigPerMut.Rd ├── cosSim.Rd ├── detSmnvType.Rd ├── extractSigsDbs.Rd ├── extractSigsIndel.Rd ├── extractSigsSnv.Rd ├── extractSigsSv.Rd ├── fitToSignatures.Rd ├── getContextsSv.Rd ├── getInfoValues.Rd ├── indelSeqFlanksStartEnd.Rd ├── lsqnonneg.Rd ├── nBasesMH.Rd ├── nCopiesAlongFlank.Rd ├── plotContexts.Rd ├── readSigsAsDf.Rd ├── readVcfFields.Rd ├── splitDfRegex.Rd ├── subsetSmnvs.Rd ├── transformContexts.Rd └── variantsFromVcf.Rd /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UMCUGenetics/mutSigExtractor/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UMCUGenetics/mutSigExtractor/HEAD/LICENSE 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