SomaticSignatures-package	SomaticSignatures-package
assessNumberSignatures	number-signatures
cluster-spectrum	cluster-spetrum
clusterSpectrum	cluster-spetrum
decomposition-signatures	decomposition-functions
dfConvertColumns	utils
findSignatures	mutational-signatures
fitted	MutationalSignatures-class
fitted,MutationalSignatures-method	MutationalSignatures-class
gcContent	gc
hs-chrs	hs-chrs
hsAllosomes	hs-chrs
hsAutosomes	hs-chrs
hsLinear	hs-chrs
hsToplevel	hs-chrs
identifySignatures	mutational-signatures
k3we	kmers-data
k3wg	kmers-data
kmerFrequency	kmers
kmers	kmers-data
kmers-data	kmers-data
motifMatrix	motif-functions
mutational-normalization	mutational-normalization
mutational-plots	mutational-plots
mutational-signatures	mutational-signatures
MutationalSignatures	MutationalSignatures-class
MutationalSignatures-class	MutationalSignatures-class
mutationContext	mutation-context
mutationContextH5vc	mutation-context
mutationContextMutect	mutation-context
mutationDistance	mutation-distribution
ncbi	granges-utils
nmfDecomposition	decomposition-functions
nmfSignatures	decomposition-functions
normalizeMotifs	mutational-normalization
observed	MutationalSignatures-class
observed,MutationalSignatures-method	MutationalSignatures-class
pcaDecomposition	decomposition-functions
pcaSignatures	decomposition-functions
plotFittedSpectrum	signature-plot-functions
plotMutationSpectrum	signature-plot-functions
plotNumberSignatures	number-signatures
plotObservedSpectrum	signature-plot-functions
plotRainfall	mutation-distribution
plotSampleMap	signature-plot-functions
plotSamples	signature-plot-functions
plotSignatureMap	signature-plot-functions
plotSignatures	signature-plot-functions
plotVariantAbundance	mutational-plots
readMutect	mutect
samples	MutationalSignatures-class
samples,MutationalSignatures-method	MutationalSignatures-class
sca-data	sca-data
scaSNVRanges	sca-vranges
sca_mm	sca-data
sca_sigs	sca-data
seqchar	granges-utils
show	MutationalSignatures-class
show,MutationalSignatures-method	MutationalSignatures-class
signatures	MutationalSignatures-class
signatures,MutationalSignatures-method	MutationalSignatures-class
signatures21	signatures21-data
signatures21-data	signatures21-data
sigs_nmf	sca-data
sigs_pca	sca-data
SomaticSignatures	SomaticSignatures-package
ucsc	granges-utils
variants-utils	utils
