YAPSA

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see YAPSA.

Yet Another Package for Signature Analysis


Bioconductor version: 3.9

This package provides functions and routines useful in the analysis of somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, functions to perform a signature analysis with known signatures (LCD = linear combination decomposition) and a signature analysis on stratified mutational catalogue (SMC = stratify mutational catalogue) are provided.

Author: Daniel Huebschmann, Zuguang Gu, Matthias Schlesner

Maintainer: Daniel Huebschmann <huebschmann.daniel at googlemail.com>

Citation (from within R, enter citation("YAPSA")):

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("YAPSA")

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("YAPSA")
YAPSA HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BiologicalQuestion, Clustering, DNASeq, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization
Version 1.10.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL-3
Depends R (>= 3.3.0), GenomicRanges, ggplot2, grid
Imports lsei, SomaticSignatures, VariantAnnotation, GenomeInfoDb, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, PMCMR, ComplexHeatmap, KEGGREST, grDevices
System Requirements
URL
See More
Suggests BSgenome.Hsapiens.UCSC.hg19, testthat, BiocStyle, knitr, rmarkdown
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Package Archives

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

Source Package YAPSA_1.10.0.tar.gz
Windows Binary YAPSA_1.10.0.zip
Mac OS X 10.11 (El Capitan) YAPSA_1.9.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/YAPSA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/YAPSA
Bioc Package Browser https://code.bioconductor.org/browse/YAPSA/
Package Short Url https://bioconductor.org/packages/YAPSA/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive