YAPSA

DOI: 10.18129/B9.bioc.YAPSA    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see YAPSA.

Yet Another Package for Signature Analysis

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") 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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("YAPSA")

 

HTML	R Script	YAPSA
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiologicalQuestion, Clustering, DNASeq, GenomicVariation, Sequencing, Software, SomaticMutation, StatisticalMethod, Visualization
Version	1.8.0
In Bioconductor since	BioC 3.4 (R-3.3) (2.5 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

Package Archives

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

Source Package	YAPSA_1.8.0.tar.gz
Windows Binary	YAPSA_1.8.0.zip
Mac OS X 10.11 (El Capitan)	YAPSA_1.8.0.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	http://bioconductor.org/packages/YAPSA/
Package Downloads Report	Download Stats