YAPSA

DOI:10.18129 / B9.bioc.YAPSA

这个包是3.15版本Bioconductor;的稳定,最新的发布版本,请参阅YAPSA。

另一个包进行签名分析

Bioconductor版本:3.15

这个包提供了监督功能和例程的分析(即突变签名。,the signatures have to be known, cf. L. Alexandrov et al., Nature 2013 and L. Alexandrov et al., Bioaxiv 2018). In particular, the family of functions LCD (LCD = linear combination decomposition) can use optimal signature-specific cutoffs which takes care of different detectability of the different signatures. Moreover, the package provides different sets of mutational signatures, including the COSMIC and PCAWG SNV signatures and the PCAWG Indel signatures; the latter infering that with YAPSA, the concept of supervised analysis of mutational signatures is extended to Indel signatures. YAPSA also provides confidence intervals as computed by profile likelihoods and can perform signature analysis on a stratified mutational catalogue (SMC = stratify mutational catalogue) in order to analyze enrichment and depletion patterns for the signatures in different strata.

作者:丹尼尔Huebschmann (aut (cre), Lea Jopp-Saile (aut),卡罗琳安德森(aut) Zuguang Gu (aut),马提亚Schlesner (aut)

维护人员:丹尼尔Huebschmann < Huebschmann。丹尼尔:googlemail.com >

安装

安装这个包,开始R(版本“4.2”)并输入:

如果(!要求(“BiocManager”,悄悄地= TRUE)) install.packages (“BiocManager”) BiocManager::安装(“YAPSA”)

R的旧版本,请参考适当的Bioconductor释放。

文档

查看文档的版本这个包安装在您的系统,开始R和输入:

browseVignettes (“YAPSA”)

HTML	R脚本	1。使用YAPSA
HTML	R脚本	2。Signature-specific达标
HTML	R脚本	3所示。置信区间
HTML	R脚本	4所示。分层分析突变的签名
HTML	R脚本	5。Indel特征分析
HTML	R脚本	6。使用YAPSA韦斯数据
HTML		index . html
PDF		参考手册
文本		新闻

细节

biocViews	BiologicalQuestion,聚类,DNASeq,GenomicVariation,测序,软件,SomaticMutation,StatisticalMethod,可视化
版本	1.22.0
Bioconductor自	BioC 3.4 (r - 3.3)(6年)
许可证	GPL-3
取决于	R (> = 3.6.0),GenomicRanges,ggplot2、网格
进口	limSolve,SomaticSignatures,VariantAnnotation,GenomeInfoDb,reshape2,gridExtra,corrplot,dendextend,GetoptLong,circlize,gtrellis,doParallel,PMCMRplus,ggbeeswarm,ComplexHeatmap,KEGGRESTgrDevices,Biostrings,BSgenome.Hsapiens.UCSC.hg19,magrittr,pracma,dplyr,跑龙套
链接
建议	testthat,BiocStyle,knitr,rmarkdown
SystemRequirements
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构建报告

包档案

遵循bob 体育网址 指示在R会话中使用这个包。

源包	YAPSA_1.22.0.tar.gz
Windows二进制	YAPSA_1.22.0.zip(64位)
macOS二进制(x86_64)	YAPSA_1.22.0.tgz
源库	git克隆https://git.bioconductor.org/packages/YAPSA
源库(开发人员访问)	git克隆git@git.bioconductor.org:包/ YAPSA
包短Url	//www.anjoumacpherson.com/packages/YAPSA/
包下载报告	下载数据