YAPSA

DOI:10.18129/B9.bioc.YAPSA

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, seeYAPSA.

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

Installation

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 appropriateBioconductor release.

Documentation

查看文档的版本包age 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	1.10.0
In Bioconductor since	BioC 3.4 (R-3.3) (3 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

Followbob 体育网址 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
Package Short Url	//www.anjoumacpherson.com/packages/YAPSA/
Package Downloads Report	Download Stats