This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see YAPSA.
Bioconductor version: 3.10
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")
):
To install this package, start R (version "3.6") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("YAPSA")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("YAPSA")
HTML | R Script | YAPSA |
Reference Manual | ||
Text | NEWS |
biocViews | BiologicalQuestion, Clustering, DNASeq, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization |
Version | 1.12.0 |
In Bioconductor since | BioC 3.4 (R-3.3) (3.5 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 |
LinkingTo | |
Suggests | BSgenome.Hsapiens.UCSC.hg19, testthat, BiocStyle, knitr, rmarkdown |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | YAPSA_1.12.0.tar.gz |
Windows Binary | YAPSA_1.12.0.zip |
Mac OS X 10.11 (El Capitan) | YAPSA_1.12.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/YAPSA |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/YAPSA |
Package Short Url | https://bioconductor.org/packages/YAPSA/ |
Package Downloads Report | Download Stats |
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