SigsPack

DOI: 10.18129/B9.bioc.SigsPack    

This is the development version of SigsPack; to use it, please install the devel version of Bioconductor.

Mutational Signature Estimation for Single Samples

Bioconductor version: Development (3.10)

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 "3.6") and enter:

if (!requireNamespace("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")

 

HTML R Script Introduction to SigsPack
PDF   Reference Manual
Text   NEWS

Details

biocViews BiomedicalInformatics, DNASeq, SNP, Software, SomaticMutation, VariantAnnotation
Version 0.99.3
In Bioconductor since BioC 3.10 (R-3.6)
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_0.99.3.tar.gz
Windows Binary SigsPack_0.99.3.zip
Mac OS X 10.11 (El Capitan) SigsPack_0.99.3.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 http://bioconductor.org/packages/SigsPack/
Package Downloads Report Download Stats

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