SigsPack

DOI: 10.18129/B9.bioc.SigsPack    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SigsPack.

Mutational Signature Estimation for Single Samples

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

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

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")

 

HTML	R Script	Introduction to SigsPack
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiomedicalInformatics, DNASeq, SNP, Software, SomaticMutation, VariantAnnotation
Version	1.4.0
In Bioconductor since	BioC 3.10 (R-3.6) (1.5 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
LinkingTo
Suggests	IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/bihealth/SigsPack
BugReports	https://github.com/bihealth/SigsPack/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SigsPack_1.4.0.tar.gz
Windows Binary	SigsPack_1.4.0.zip
macOS 10.13 (High Sierra)	SigsPack_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SigsPack
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SigsPack
Package Short Url	https://bioconductor.org/packages/SigsPack/
Package Downloads Report	Download Stats