decompTumor2Sig

DOI: 10.18129/B9.bioc.decompTumor2Sig    

This is the development version of decompTumor2Sig; to use it, please install the devel version of Bioconductor.

Decomposition of individual tumors into mutational signatures by signature refitting

Bioconductor version: Development (3.10)

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>

Citation (from within R, enter citation("decompTumor2Sig")):

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("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 2.1.0
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_2.1.0.tar.gz
Windows Binary decompTumor2Sig_2.1.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) decompTumor2Sig_2.1.0.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 http://bioconductor.org/packages/decompTumor2Sig/
Package Downloads Report Download Stats

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