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("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 | ||
| 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 |
| 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 | 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 |