SomaticSignatures: Somatic Signatures
Version 2.12.1

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
Bioconductor views Clustering GenomicVariation Sequencing SomaticMutation StatisticalMethod Visualization
Date of publicationNone
MaintainerJulian Gehring <jg-bioc@gmx.com>
LicenseMIT + file LICENSE
Version2.12.1
URL https://github.com/juliangehring/SomaticSignatures
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SomaticSignatures")

Getting started

Package overview

Popular man pages

cluster-spetrum: Cluster Mutational Spectrum
granges-utils: GRanges converter functions
mutational-signatures: Estimate Somatic Signatures
MutationalSignatures-class: 'MutationalSignatures' class and methods
mutation-context: mutationContext functions
mutect: readMutect
signature-plot-functions: Plot Mutational Signatures
See all...

All man pages Function index File listing

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
MutationalSignatures-class: 'MutationalSignatures' class and methods
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

Functions

MutationalSignatures Man page
MutationalSignatures-class Man page
SomaticSignatures Man page
SomaticSignatures-package Man page
assessNumberSignatures Man page Source code
assessOneSignature Source code
cluster-spectrum Man page
clusterSpectrum Man page Source code
constructMotifs3 Source code
correlateSignatures Source code
coscor Source code
cospos Source code
cossim Source code
decomposition-signatures Man page
dfConvertColumns Man page Source code
findSignatures Man page Source code
fitted Man page
fitted,MutationalSignatures-method Man page
gcContent Man page Source code
hs-chrs Man page
hsAllosomes Man page Source code
hsAutosomes Man page Source code
hsLinear Man page Source code
hsToplevel Man page Source code
identifySignatures Man page Source code
identifySignaturesVRanges Source code
k3we Man page
k3wg Man page
kmeansDecomposition Source code
kmeansSignatures Source code
kmerFrequency Man page Source code
kmers Man page
kmers-data Man page
meltSignatures Source code
motifMatrix Man page Source code
mutationContext Man page Source code
mutationContextMutect Man page Source code
mutationDistance Man page Source code
mutational-normalization Man page
mutational-plots Man page
mutational-signatures Man page
ncbi Man page Source code
nmfDecomposition Man page Source code
nmfSignatures Man page Source code
normalizeMotifs Man page Source code
observed Man page
observed,MutationalSignatures-method Man page
pcaDecomposition Man page Source code
pcaSignatures Man page Source code
plotFittedSpectrum Man page Source code
plotMutationSpectrum Man page Source code
plotNumberSignatures Man page Source code
plotObservedSpectrum Man page Source code
plotRainfall Man page Source code
plotSampleMap Man page Source code
plotSamples Man page Source code
plotSignatureMap Man page Source code
plotSignatures Man page Source code
plotSpectrum Source code
plotVariantAbundance Man page Source code
readMutect Man page Source code
retreiveSignatures Source code
samples Man page
samples,MutationalSignatures-method Man page
sca-data Man page
sca_mm Man page
sca_motifs_tiny Man page
sca_sigs Man page
seqchar Man page Source code
show Man page
show,MutationalSignatures-method Man page
showSome Source code
signatureLabels Source code
signatures Man page
signatures,MutationalSignatures-method Man page
signatures21 Man page
signatures21-data Man page
sigs_nmf Man page
sigs_pca Man page
theme_small_axis Source code
theme_ss Source code
ucsc Man page Source code
variants-utils Man page

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/classes.R
R/cluster.R
R/correlate.R
R/decomposition.R
R/gc.R
R/granges-utils.R
R/hs-chrs.R
R/kmers.R
R/motif-matrix.R
R/mutation-context.R
R/mutational-plots.R
R/mutational-signatures.R
R/mutect.R
R/normalize.R
R/number-signatures.R
R/rainfall.R
R/signature-plots.R
R/utils.R
build
build/vignette.rds
data
data/kmers.rda
data/sca_mm.rda
data/sca_motifs_tiny.rda
data/sca_sigs.rda
data/signatures21.rda
inst
inst/CITATION
inst/css
inst/css/bioc.css
inst/doc
inst/doc/SomaticSignatures-vignette.R
inst/doc/SomaticSignatures-vignette.Rhtml
inst/doc/SomaticSignatures-vignette.html
inst/examples
inst/examples/mutect.tsv
inst/scripts
inst/scripts/kmers-data.R
inst/signatures
inst/signatures/signatures.txt
man
man/MutationalSignatures-class.rd
man/SomaticSignatures-package.Rd
man/cluster-spetrum.Rd
man/decomposition-functions.Rd
man/gc.Rd
man/granges-utils.Rd
man/hs-chrs.Rd
man/kmers-data.Rd
man/kmers.Rd
man/motif-functions.Rd
man/mutation-context.Rd
man/mutation-distribution.Rd
man/mutational-normalization.Rd
man/mutational-plots.Rd
man/mutational-signatures.Rd
man/mutect.Rd
man/number-signatures.Rd
man/sca-data.Rd
man/signature-plot-functions.Rd
man/signatures21-data.Rd
man/utils.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test-SomaticSignatures.R
vignettes
vignettes/SomaticSignatures-vignette.Rhtml
vignettes/SomaticSignatures-vignette.org
vignettes/bioc.css
vignettes/references.bib
vignettes/references.html
SomaticSignatures documentation built on May 24, 2017, 2 a.m.

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