SparseSignatures
SparseSignatures
Bioconductor version: 3.23 · Package version: 2.22.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SparseSignatures")Details
| Maintainer | Luca De Sano <luca.desano@gmail.com> |
| Author | Daniele Ramazzotti [aut] (ORCID: <https://orcid.org/0000-0002-6087-2666>), Avantika Lal [aut], Keli Liu [ctb], Luca De Sano [cre, aut] (ORCID: <https://orcid.org/0000-0002-9618-3774>), Robert Tibshirani [ctb], Arend Sidow [aut] |
| License | file LICENSE |
| URL | https://github.com/danro9685/SparseSignatures |
| Bug Reports | https://github.com/danro9685/SparseSignatures |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | BiomedicalInformatics, Software, SomaticMutation |
| Package Short Url | https://bioconductor.org/packages/SparseSignatures/ |
Citation
From within R, enter citation("SparseSignatures"):
Daniele Ramazzotti, Avantika Lal, Luca De Sano, Arend Sidow. SparseSignatures: SparseSignatures. doi:10.18129/B9.bioc.SparseSignatures, R package version 2.22.0, https://bioconductor.org/packages/SparseSignatures.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SparseSignatures_2.22.0.tar.gz |
| Windows binary (x86_64) | SparseSignatures_2.22.0.zip |
| macOS binary (arm64) | SparseSignatures_2.22.0.tgz |
| macOS binary (x86_64) | SparseSignatures_2.22.0.tgz |
Dependencies
Depends: R (>= 4.1.0), NMF
Imports: nnlasso, nnls, parallel, data.table, Biostrings, GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2, gridExtra, reshape2, RhpcBLASctl
Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr