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
SigsPack_1.21.0.zip(r-4.5)SigsPack_1.21.0.zip(r-4.4)SigsPack_1.21.0.zip(r-4.3)
SigsPack_1.21.0.tgz(r-4.4-any)SigsPack_1.21.0.tgz(r-4.3-any)
SigsPack_1.21.0.tar.gz(r-4.5-noble)SigsPack_1.21.0.tar.gz(r-4.4-noble)
SigsPack_1.21.0.tgz(r-4.4-emscripten)SigsPack_1.21.0.tgz(r-4.3-emscripten)
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'))

Peer review:

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 163 downloads 1 mentions 9 exports 72 dependencies

Last updated 2 months agofrom:7943dfb283. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-winOKNov 30 2024
R-4.5-linuxOKNov 30 2024
R-4.4-winOKNov 30 2024
R-4.4-macOKNov 30 2024
R-4.3-winOKNov 30 2024
R-4.3-macOKNov 30 2024

Exports:bootstrap_mut_cataloguescreate_mut_cataloguesdecomposeQPget_context_freqnormalizeplot_bootstrapped_exposuresignature_exposuresummarize_exposuresvcf2mut_cat

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngquadprogR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsVariantAnnotationvctrsXMLXVectoryamlzlibbioc

Introduction to SigsPack

Rendered fromSigsPack.Rmdusingknitr::rmarkdownon Nov 30 2024.

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