Package: SigsPack 1.21.0

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_1.21.0.tar.gz
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SigsPack.pdf |SigsPack.html✨
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-1.21.0(bioc 3.21)SigsPack-1.20.0(bioc 3.20)

somaticmutationsnpvariantannotationbiomedicalinformaticsdnaseq

4.30 score 2 stars 4 scripts 194 downloads 1 mentions 9 exports 71 dependencies

Last updated 4 months agofrom:7943dfb283. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 29 2025
R-4.5-winOKJan 29 2025
R-4.5-macOKJan 29 2025
R-4.5-linuxOKJan 29 2025
R-4.4-winOKJan 29 2025
R-4.4-macOKJan 29 2025
R-4.3-winOKJan 29 2025
R-4.3-macOKJan 29 2025

Exports:bootstrap_mut_cataloguescreate_mut_cataloguesdecomposeQPget_context_freqnormalizeplot_bootstrapped_exposuresignature_exposuresummarize_exposuresvcf2mut_cat

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngquadprogR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsVariantAnnotationvctrsXMLXVectoryaml

Introduction to SigsPack

Rendered fromSigsPack.Rmdusingknitr::rmarkdownon Jan 29 2025.

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