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