decompTumor2Sig

This is the released version of decompTumor2Sig; for the devel version, see decompTumor2Sig.

Decomposition of individual tumors into mutational signatures by signature refitting

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.decompTumor2Sig

Bioconductor version: Release (3.22)

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 "4.5") and enter:


if (!require("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")

A brief introduction to decompTumor2Sig HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BiologicalQuestion, BiomedicalInformatics, DNASeq, Genetics, GenomicVariation, SNP, Sequencing, Software, SomaticMutation, StatisticalMethod

Version 2.26.0

In Bioconductor since BioC 3.9 (R-3.6) (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, Seqinfo, readxl

System Requirements

URL http://rmpiro.net/decompTumor2Sig/ https://github.com/rmpiro/decompTumor2Sig

Bug Reports https://github.com/rmpiro/decompTumor2Sig/issues

Suggests knitr, rmarkdown, BiocStyle

Linking To

Enhances

Depends On Me

Imports Me musicatk

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package decompTumor2Sig_2.26.0.tar.gz

Windows Binary (x86_64) decompTumor2Sig_2.25.1.zip (64-bit only)

macOS Binary (x86_64) decompTumor2Sig_2.26.0.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