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Bioconductor - SigsPack (development version)

SigsPack

This is the development version of SigsPack; for the stable release version, see SigsPack.

Mutational Signature Estimation for Single Samples

Bioconductor version: Development (3.22)

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.

Author: Franziska Schumann <franziska.schumann at student.hpi.de>

Maintainer: Franziska Schumann <franziska.schumann at student.hpi.de>

Citation (from within R, enter citation("SigsPack")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SigsPack")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SigsPack")
Details biocViews BiomedicalInformatics, DNASeq, SNP, Software, SomaticMutation, VariantAnnotation Version 1.23.0 In Bioconductor since BioC 3.10 (R-3.6) (5.5 years) License GPL-3 Depends R (>= 3.6) Imports quadprog (>= 1.5-5), methods, Biobase, BSgenome(>= 1.46.0), VariantAnnotation(>= 1.24.5), Biostrings, GenomeInfoDb, GenomicRanges, rtracklayer, SummarizedExperiment, graphics, stats, utils System Requirements URL https://github.com/bihealth/SigsPack Bug Reports https://github.com/bihealth/SigsPack/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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