decompTumor2Sig
This is the released version of decompTumor2Sig; for the devel version, see decompTumor2Sig.
Decomposition of individual tumors into mutational signatures by signature refitting
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 2.28.1 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 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 |
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_2.28.1.tar.gz |
| Windows Binary (x86_64) | decompTumor2Sig_2.28.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | decompTumor2Sig_2.28.0.tgz |
| macOS Binary (sonoma-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 |
| Old Source Packages for BioC 3.23 | Source Archive |