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.

Author
Julian Gehring
Date of publication
None
Maintainer
Julian Gehring <jg-bioc@gmx.com>
License
MIT + file LICENSE
Version
2.10.0
URLs

View on Bioconductor

Man pages

cluster-spetrum
Cluster Mutational Spectrum
decomposition-functions
Decomposition Functions for Somatic Signatures
gc
GC Content
granges-utils
GRanges converter functions
hs-chrs
Human Chromosome Names
kmers
Kmer Frequency
kmers-data
Kmer datasets
motif-functions
Group somatic moticfs
mutational-normalization
Normalize Somatic Motifs
mutational-plots
Mutational Plots
mutational-signatures
Estimate Somatic Signatures
mutation-context
mutationContext functions
mutation-distribution
Distributions of mutational locations.
mutect
readMutect
number-signatures
Number of Signatures
sca-data
SomaticCancerAlterations Results
signature-plot-functions
Plot Mutational Signatures
signatures21-data
21 Signatures
SomaticSignatures-package
SomaticSignatures package
utils
Utility functions

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