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SparseSignatures

This is the development version of SparseSignatures; for the stable release version, see SparseSignatures.

SparseSignatures


Bioconductor version: Development (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 (from within R, enter citation("SparseSignatures")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text
LICENSE Text

Details

biocViews BiomedicalInformatics, Software, SomaticMutation
Version 2.13.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
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Depends On Me
Imports Me
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Package Archives

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

Source Package SparseSignatures_2.13.0.tar.gz
Windows Binary SparseSignatures_2.13.0.zip
macOS Binary (x86_64) SparseSignatures_2.13.0.tgz
macOS Binary (arm64) SparseSignatures_2.13.0.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