This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

decompTumor2Sig

Decomposition of individual tumors into mutational signatures by signature refitting

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews BiologicalQuestion, BiomedicalInformatics, DNASeq, Genetics, GenomicVariation, SNP, Sequencing, Software, SomaticMutation, StatisticalMethod
Version 2.16.0
In Bioconductor since BioC 3.9 (R-3.6) (4.5 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
Linking To
Suggests knitr, rmarkdown, BiocStyle
System Requirements
Enhances
URL http://rmpiro.net/decompTumor2Sig/ https://github.com/rmpiro/decompTumor2Sig
Bug Reports https://github.com/rmpiro/decompTumor2Sig/issues
See More
Depends On Me
Imports Me musicatk
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package decompTumor2Sig_2.16.0.tar.gz
Windows Binary decompTumor2Sig_2.16.0.zip (64-bit only)
macOS Binary (x86_64) decompTumor2Sig_2.16.0.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