SparseSignatures
SparseSignatures
Bioconductor version: Release (3.19)
Point mutations occurring in a genome can be divided into 96 categories based on the base being mutated, the base it is mutated into and its two flanking bases. Therefore, for any patient, it is possible to represent all the point mutations occurring in that patient's tumor as a vector of length 96, where each element represents the count of mutations for a given category in the patient. A mutational signature represents the pattern of mutations produced by a mutagen or mutagenic process inside the cell. Each signature can also be represented by a vector of length 96, where each element represents the probability that this particular mutagenic process generates a mutation of the 96 above mentioned categories. In this R package, we provide a set of functions to extract and visualize the mutational signatures that best explain the mutation counts of a large number of patients.
Author: Daniele Ramazzotti [aut] 
, Avantika Lal [aut], Keli Liu [ctb], Luca De Sano [cre, aut] , Robert Tibshirani [ctb], Arend Sidow [aut]
Maintainer: Luca De Sano <luca.desano at gmail.com>
citation("SparseSignatures")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SparseSignatures")
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("SparseSignatures")| v1_introduction.html | HTML | |
| v2_using_the_package.html | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiomedicalInformatics, Software, SomaticMutation |
| Version | 2.14.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6.5 years) |
| License | file LICENSE |
| Depends | R (>= 4.1.0), NMF |
| Imports | nnlasso, nnls, parallel, data.table, Biostrings, GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2, gridExtra, reshape2 |
| System Requirements | |
| URL | https://github.com/danro9685/SparseSignatures |
| Bug Reports | https://github.com/danro9685/SparseSignatures |
See More
| Suggests | BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr |
| 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 | SparseSignatures_2.14.0.tar.gz |
| Windows Binary (x86_64) | SparseSignatures_2.14.0.zip (64-bit only) |
| macOS Binary (x86_64) | SparseSignatures_2.14.0.tgz |
| macOS Binary (arm64) | SparseSignatures_2.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SparseSignatures |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SparseSignatures |
| Bioc Package Browser | https://code.bioconductor.org/browse/SparseSignatures/ |
| Package Short Url | https://bioconductor.org/packages/SparseSignatures/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |