SomaticSignatures: Somatic Signatures

The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.

AuthorJulian Gehring
Date of publicationNone
MaintainerJulian Gehring <jg-bioc@gmx.com>
LicenseMIT + file LICENSE
Version2.10.0
https://github.com/juliangehring/SomaticSignatures

View on Bioconductor

Functions

assessNumberSignatures Man page
cluster-spectrum Man page
clusterSpectrum Man page
decomposition-signatures Man page
dfConvertColumns Man page
findSignatures Man page
gcContent Man page
hsAllosomes Man page
hsAutosomes Man page
hs-chrs Man page
hsLinear Man page
hsToplevel Man page
identifySignatures Man page
k3we Man page
k3wg Man page
kmerFrequency Man page
kmers Man page
kmers-data Man page
motifMatrix Man page
mutational-normalization Man page
mutational-plots Man page
mutational-signatures Man page
mutationContext Man page
mutationContextMutect Man page
mutationDistance Man page
ncbi Man page
nmfDecomposition Man page
nmfSignatures Man page
normalizeMotifs Man page
pcaDecomposition Man page
pcaSignatures Man page
plotFittedSpectrum Man page
plotMutationSpectrum Man page
plotNumberSignatures Man page
plotObservedSpectrum Man page
plotRainfall Man page
plotSampleMap Man page
plotSamples Man page
plotSignatureMap Man page
plotSignatures Man page
plotVariantAbundance Man page
readMutect Man page
sca-data Man page
sca_mm Man page
sca_motifs_tiny Man page
sca_sigs Man page
seqchar Man page
signatures21 Man page
signatures21-data Man page
sigs_nmf Man page
sigs_pca Man page
SomaticSignatures Man page
SomaticSignatures-package Man page
ucsc Man page
variants-utils Man page

Files

SomaticSignatures/DESCRIPTION
SomaticSignatures/LICENSE
SomaticSignatures/NAMESPACE
SomaticSignatures/NEWS
SomaticSignatures/R
SomaticSignatures/R/classes.R SomaticSignatures/R/cluster.R SomaticSignatures/R/correlate.R SomaticSignatures/R/decomposition.R SomaticSignatures/R/gc.R SomaticSignatures/R/granges-utils.R SomaticSignatures/R/hs-chrs.R SomaticSignatures/R/kmers.R SomaticSignatures/R/motif-matrix.R SomaticSignatures/R/mutation-context.R SomaticSignatures/R/mutational-plots.R SomaticSignatures/R/mutational-signatures.R SomaticSignatures/R/mutect.R SomaticSignatures/R/normalize.R SomaticSignatures/R/number-signatures.R SomaticSignatures/R/rainfall.R SomaticSignatures/R/signature-plots.R SomaticSignatures/R/utils.R
SomaticSignatures/build
SomaticSignatures/build/vignette.rds
SomaticSignatures/data
SomaticSignatures/data/kmers.rda
SomaticSignatures/data/sca_mm.rda
SomaticSignatures/data/sca_motifs_tiny.rda
SomaticSignatures/data/sca_sigs.rda
SomaticSignatures/data/signatures21.rda
SomaticSignatures/inst
SomaticSignatures/inst/CITATION
SomaticSignatures/inst/css
SomaticSignatures/inst/css/bioc.css
SomaticSignatures/inst/doc
SomaticSignatures/inst/doc/SomaticSignatures-vignette.R
SomaticSignatures/inst/doc/SomaticSignatures-vignette.Rhtml
SomaticSignatures/inst/doc/SomaticSignatures-vignette.html
SomaticSignatures/inst/examples
SomaticSignatures/inst/examples/mutect.tsv
SomaticSignatures/inst/scripts
SomaticSignatures/inst/scripts/kmers-data.R
SomaticSignatures/inst/signatures
SomaticSignatures/inst/signatures/signatures.txt
SomaticSignatures/man
SomaticSignatures/man/MutationalSignatures-class.rd
SomaticSignatures/man/SomaticSignatures-package.Rd SomaticSignatures/man/cluster-spetrum.Rd SomaticSignatures/man/decomposition-functions.Rd SomaticSignatures/man/gc.Rd SomaticSignatures/man/granges-utils.Rd SomaticSignatures/man/hs-chrs.Rd SomaticSignatures/man/kmers-data.Rd SomaticSignatures/man/kmers.Rd SomaticSignatures/man/motif-functions.Rd SomaticSignatures/man/mutation-context.Rd SomaticSignatures/man/mutation-distribution.Rd SomaticSignatures/man/mutational-normalization.Rd SomaticSignatures/man/mutational-plots.Rd SomaticSignatures/man/mutational-signatures.Rd SomaticSignatures/man/mutect.Rd SomaticSignatures/man/number-signatures.Rd SomaticSignatures/man/sca-data.Rd SomaticSignatures/man/signature-plot-functions.Rd SomaticSignatures/man/signatures21-data.Rd SomaticSignatures/man/utils.Rd
SomaticSignatures/tests
SomaticSignatures/tests/testthat
SomaticSignatures/tests/testthat.R
SomaticSignatures/tests/testthat/test-SomaticSignatures.R
SomaticSignatures/vignettes
SomaticSignatures/vignettes/SomaticSignatures-vignette.Rhtml
SomaticSignatures/vignettes/SomaticSignatures-vignette.org
SomaticSignatures/vignettes/bioc.css
SomaticSignatures/vignettes/references.bib
SomaticSignatures/vignettes/references.html

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.