To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("YAPSA")
In most cases, you don't need to download the package archive at all.
YAPSA
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see YAPSA.
Yet Another Package for Signature Analysis
Bioconductor version: 3.4
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("YAPSA")
Documentation
| HTML | R Script | YAPSA |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | BiologicalQuestion, Clustering, DNASeq, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (0.5 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | YAPSA_1.0.0.tar.gz |
| Windows Binary | YAPSA_1.0.0.zip |
| Mac OS X 10.9 (Mavericks) | YAPSA_1.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/YAPSA/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/YAPSA/ |
| Package Downloads Report | Download Stats |
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