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

Files in this package

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.

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