Package: SigsPack 1.27.0

Franziska Schumann

SigsPack: Mutational Signature Estimation for Single Samples

Single sample estimation of exposure to mutational signatures. Exposures to known mutational signatures are estimated for single samples, based on quadratic programming algorithms. Bootstrapping the input mutational catalogues provides estimations on the stability of these exposures. The effect of the sequence composition of mutational context can be taken into account by normalising the catalogues.

Authors:Franziska Schumann <[email protected]>

SigsPack_1.27.0.tar.gz
SigsPack_1.27.0.zip(r-4.7)SigsPack_1.27.0.zip(r-4.6)SigsPack_1.27.0.zip(r-4.5)
SigsPack_1.27.0.tgz(r-4.6-any)SigsPack_1.27.0.tgz(r-4.5-any)
SigsPack_1.27.0.tar.gz(r-4.7-any)SigsPack_1.27.0.tar.gz(r-4.6-any)
SigsPack_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SigsPack/json (API)
NEWS

# Install 'SigsPack' in R:
install.packages('SigsPack', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bihealth/sigspack/issues

Datasets:

On BioConductor:SigsPack-1.27.0(bioc 3.24)SigsPack-1.26.0(bioc 3.23)

somaticmutationsnpvariantannotationbiomedicalinformaticsdnaseq

4.30 score 2 stars 5 scripts 358 downloads 1 mentions 9 exports 72 dependencies

Last updated from:c0b05f0f0a. Checks:1 ERROR, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR206
linux-devel-x86_64OK291
source / vignettesOK311
linux-release-x86_64OK303
macos-release-arm64OK226
macos-oldrel-arm64OK229
windows-develOK265
windows-releaseOK322
windows-oldrelOK333
wasm-releaseOK176

Exports:bootstrap_mut_cataloguescreate_mut_cataloguesdecomposeQPget_context_freqnormalizeplot_bootstrapped_exposuresignature_exposuresummarize_exposuresvcf2mut_cat

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngquadprogR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysUCSC.utilsVariantAnnotationvctrsXMLXVectoryaml

Introduction to SigsPack

Rendered fromSigsPack.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2019-08-15
Started: 2019-04-09