decompTumor2Sig

DOI: 10.18129/B9.bioc.decompTumor2Sig    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see decompTumor2Sig.

Decomposition of individual tumors into mutational signatures by signature refitting

Bioconductor version: 3.9

Uses quadratic programming for signature refitting, i.e., to decompose the mutation catalog from an individual tumor sample into a set of given mutational signatures (either Alexandrov-model signatures or Shiraishi-model signatures), computing weights that reflect the contributions of the signatures to the mutation load of the tumor.

Author: Rosario M. Piro [aut, cre], Sandra Krueger [ctb]

Maintainer: Rosario M. Piro <rmpiro at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("decompTumor2Sig")

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("decompTumor2Sig")

 

HTML	R Script	A brief introduction to decompTumor2Sig
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiologicalQuestion, BiomedicalInformatics, DNASeq, Genetics, GenomicVariation, SNP, Sequencing, Software, SomaticMutation, StatisticalMethod
Version	2.0.0
In Bioconductor since	BioC 3.9 (R-3.6) (< 6 months)
License	GPL-2
Depends	R (>= 3.6), ggplot2
Imports	methods, Matrix, quadprog (>= 1.5-5), vcfR, GenomicRanges, stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	http://rmpiro.net/decompTumor2Sig/ https://github.com/rmpiro/decompTumor2Sig
BugReports	https://github.com/rmpiro/decompTumor2Sig/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	decompTumor2Sig_2.0.0.tar.gz
Windows Binary	decompTumor2Sig_2.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	decompTumor2Sig_2.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/decompTumor2Sig
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/decompTumor2Sig
Package Short Url	https://bioconductor.org/packages/decompTumor2Sig/
Package Downloads Report	Download Stats