SparseSignatures

DOI: 10.18129/B9.bioc.SparseSignatures    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SparseSignatures.

SparseSignatures

Bioconductor version: 3.12

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 [cre, aut] , Avantika Lal [aut], Keli Liu [ctb], Luca De Sano [aut] , Robert Tibshirani [ctb], Arend Sidow [aut]

Maintainer: Luca De Sano <luca.desano at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

PDF	R Script	SparseSignatures
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BiomedicalInformatics, Software, SomaticMutation
Version	2.0.0
In Bioconductor since	BioC 3.7 (R-3.5) (3 years)
License	file LICENSE
Depends	R (>= 4.0.0), NMF
Imports	nnlasso, nnls, parallel, data.table, Biostrings, GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2, gridExtra, reshape2
LinkingTo
Suggests	BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr
SystemRequirements
Enhances
URL	https://github.com/danro9685/SparseSignatures
BugReports	https://github.com/danro9685/SparseSignatures
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SparseSignatures_2.0.0.tar.gz
Windows Binary	SparseSignatures_2.0.0.zip
macOS 10.13 (High Sierra)	SparseSignatures_2.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SparseSignatures
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SparseSignatures
Package Short Url	https://bioconductor.org/packages/SparseSignatures/
Package Downloads Report	Download Stats