decompTumor2Sig
Decomposition of individual tumors into mutational signatures by signature refitting
Bioconductor version: Release (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("decompTumor2Sig")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text |
Details
biocViews | BiologicalQuestion, BiomedicalInformatics, DNASeq, Genetics, GenomicVariation, SNP, Sequencing, Software, SomaticMutation, StatisticalMethod |
Version | 2.20.0 |
In Bioconductor since | BioC 3.9 (R-3.6) (5.5 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 |
See More
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_2.20.0.tar.gz |
Windows Binary | decompTumor2Sig_2.20.0.zip |
macOS Binary (x86_64) | decompTumor2Sig_2.20.0.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 |