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decompTumor2Sig

This is the development version of decompTumor2Sig; for the stable release version, see decompTumor2Sig.

Decomposition of individual tumors into mutational signatures by signature refitting


Bioconductor version: Development (3.19)

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

Details

biocViews BiologicalQuestion, BiomedicalInformatics, DNASeq, Genetics, GenomicVariation, SNP, Sequencing, Software, SomaticMutation, StatisticalMethod
Version 2.19.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL-2
Depends R (>= 4.0), ggplot2
Imports methods, Matrix, quadprog (>= 1.5-5), GenomicRanges, stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, SummarizedExperiment, ggseqlogo, gridExtra, data.table, GenomeInfoDb, readxl
System Requirements
URL http://rmpiro.net/decompTumor2Sig/ https://github.com/rmpiro/decompTumor2Sig
Bug Reports https://github.com/rmpiro/decompTumor2Sig/issues
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Suggests knitr, rmarkdown, BiocStyle
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Build Report Build Report

Package Archives

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

Source Package decompTumor2Sig_2.19.0.tar.gz
Windows Binary decompTumor2Sig_2.19.0.zip
macOS Binary (x86_64) decompTumor2Sig_2.19.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/decompTumor2Sig
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/decompTumor2Sig
Bioc Package Browser https://code.bioconductor.org/browse/decompTumor2Sig/
Package Short Url https://bioconductor.org/packages/decompTumor2Sig/
Package Downloads Report Download Stats