SigsPack
Mutational Signature Estimation for Single Samples
Bioconductor version: Release (3.20)
Single sample estimation of exposure to mutational signatures. Exposures to known mutational signatures are estimated for single samples, based on quadratic programming algorithms. Bootstrapping the input mutational catalogues provides estimations on the stability of these exposures. The effect of the sequence composition of mutational context can be taken into account by normalising the catalogues.
Author: Franziska Schumann <franziska.schumann at student.hpi.de>
Maintainer: Franziska Schumann <franziska.schumann at student.hpi.de>
citation("SigsPack")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SigsPack")
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("SigsPack")| Introduction to SigsPack | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, DNASeq, SNP, Software, SomaticMutation, VariantAnnotation |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (5 years) |
| License | GPL-3 |
| Depends | R (>= 3.6) |
| Imports | quadprog (>= 1.5-5), methods, Biobase, BSgenome(>= 1.46.0), VariantAnnotation(>= 1.24.5), Biostrings, GenomeInfoDb, GenomicRanges, rtracklayer, SummarizedExperiment, graphics, stats, utils |
| System Requirements | |
| URL | https://github.com/bihealth/SigsPack |
| Bug Reports | https://github.com/bihealth/SigsPack/issues |
See More
| Suggests | IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown |
| 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 | SigsPack_1.20.0.tar.gz |
| Windows Binary (x86_64) | SigsPack_1.20.0.zip |
| macOS Binary (x86_64) | SigsPack_1.20.0.tgz |
| macOS Binary (arm64) | SigsPack_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SigsPack |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SigsPack |
| Bioc Package Browser | https://code.bioconductor.org/browse/SigsPack/ |
| Package Short Url | https://bioconductor.org/packages/SigsPack/ |
| Package Downloads Report | Download Stats |