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

DOI: 10.18129/B9.bioc.YAPSA    

This is the development version of YAPSA; for the stable release version, see YAPSA.

Yet Another Package for Signature Analysis

Bioconductor version: Development (3.6)

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
PDF   Reference Manual
Text   NEWS

Details

biocViews BiologicalQuestion, Clustering, DNASeq, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization
Version 1.3.0
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
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.

Source Package YAPSA_1.3.0.tar.gz
Windows Binary YAPSA_1.3.0.zip
Mac OS X 10.11 (El Capitan) YAPSA_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/YAPSA
Package Short Url http://bioconductor.org/packages/YAPSA/
Package Downloads Report Download Stats

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