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SigsPack

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

Mutational Signature Estimation for Single Samples


Bioconductor version: Development (3.19)

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 "4.4") 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")
Introduction to SigsPack HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BiomedicalInformatics, DNASeq, SNP, Software, SomaticMutation, VariantAnnotation
Version 1.17.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
Suggests IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package SigsPack_1.17.0.tar.gz
Windows Binary SigsPack_1.17.0.zip
macOS Binary (x86_64) SigsPack_1.17.0.tgz
macOS Binary (arm64) SigsPack_1.17.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SigsPack
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SigsPack
Bioc Package Browser https://code.bioconductor.org/browse/SigsPack/
Package Short Url https://bioconductor.org/packages/SigsPack/
Package Downloads Report Download Stats