Package: SigsPack 1.26.0

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_1.26.0.tar.gz
SigsPack_1.26.0.zip(r-4.7)SigsPack_1.26.0.zip(r-4.6)SigsPack_1.26.0.zip(r-4.5)
SigsPack_1.26.0.tgz(r-4.6-any)SigsPack_1.26.0.tgz(r-4.5-any)
SigsPack_1.26.0.tar.gz(r-4.7-any)SigsPack_1.26.0.tar.gz(r-4.6-any)
SigsPack_1.26.0.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-release.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 71 dependencies

Last updated from:b916f9d8d4 (on RELEASE_3_23). Checks:1 ERROR, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR210
linux-devel-x86_64OK293
source / vignettesOK336
linux-release-x86_64OK322
macos-release-arm64OK192
macos-oldrel-arm64OK196
windows-develOK312
windows-releaseOK321
windows-oldrelOK292
wasm-releaseOK196

Exports:bootstrap_mut_cataloguescreate_mut_cataloguesdecomposeQPget_context_freqnormalizeplot_bootstrapped_exposuresignature_exposuresummarize_exposuresvcf2mut_cat

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngquadprogR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysUCSC.utilsVariantAnnotationvctrsXMLXVectoryaml

Introduction to SigsPack

Rendered fromSigsPack.Rmdusingknitr::rmarkdownon May 30 2026.

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