decompTumor2Sig
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see decompTumor2Sig.
Decomposition of individual tumors into mutational signatures by signature refitting
Bioconductor version: 3.9
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 "3.6") 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 | 2.0.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| 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 |
| 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 | |
| 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_2.0.0.tar.gz |
| Windows Binary | decompTumor2Sig_2.0.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | decompTumor2Sig_2.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/decompTumor2Sig |
| Source Repository (Developer Access) | git clone [email protected]:packages/decompTumor2Sig |
| Bioc Package Browser | https://code.bioconductor.org/browse/decompTumor2Sig/ |
| Package Short Url | https://bioconductor.org/packages/decompTumor2Sig/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |