geneXtendeR

DOI:10.18129 / B9.bioc.geneXtendeR

这是发展geneXtendeR版本;稳定的发布版本,请参阅geneXtendeR。

优化的功能注释ChIP-seq数据

Bioconductor版本:发展(3.16)

geneXtendeR优化的功能注释ChIP-seq山峰探索注释ChIP-seq峰集的相对差异基因的身体变长。之前技术相比,geneXtendeR考虑峰值不仅仅是最近的基因注释,允许用户看到峰first-closest基因的汇总统计数据,刷新率——接近基因,…,n-closest gene whilst ranking the output according to biologically relevant events and iteratively comparing the fidelity of peak-to-gene overlap across a user-defined range of upstream and downstream extensions on the original boundaries of each gene's coordinates. Since different ChIP-seq peak callers produce different differentially enriched peaks with a large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can often be a noisy process. As such, the goal of geneXtendeR is to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR.

作者:波丹Khomtchouk (aut (cre),威廉·克勒(aut)

维护人员:波丹Khomtchouk < khomtchoukmed gmail.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) #以下初始化使用Bioc猛击BiocManager::安装(version =“重击”)BiocManager::安装(“geneXtendeR”)

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 (“geneXtendeR”)

PDF		geneXtendeR.pdf
PDF		参考手册

细节

biocViews	注释,ChIPSeq,ChipOnChip,报道,DataImport,DifferentialPeakCalling,去,遗传学,GenomeAnnotation,HistoneModification,NaturalLanguageProcessing,PeakDetection,软件,可视化
版本	1.23.0
Bioconductor自	BioC 3.4 (r - 3.3)(5.5年)
许可证	GPL (> = 3)
取决于	rtracklayer,GO.dbR (> = 3.5.0)
进口	data.table,dplyr、图形、networkD3,RColorBrewer,SnowballC,tm跑龙套,wordcloud,AnnotationDbi,BiocStyle,org.Rn.eg.db
链接
建议	knitr,rmarkdown,testthat,org.Ag.eg.db,org.Bt.eg.db,org.Ce.eg.db,org.Cf.eg.db,org.Dm.eg.db,org.Dr.eg.db,org.Gg.eg.db,org.Hs.eg.db,org.Mm.eg.db,org.Pt.eg.db,org.Sc.sgd.db,org.Ss.eg.db,org.Xl.eg.db,rtracklayer
SystemRequirements
增强了
URL	https://github.com/Bohdan-Khomtchouk/geneXtendeR
BugReports	https://github.com/Bohdan-Khomtchouk/geneXtendeR/issues
取决于我
进口我
建议我
我的链接
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	geneXtendeR_1.23.0.tar.gz
Windows二进制	geneXtendeR_1.23.0.zip
macOS 10.13(高山脉)	geneXtendeR_1.23.0.tgz
源库	git克隆https://git.bioconductor.org/packages/geneXtendeR
源库(开发人员访问)	git克隆git@git.bioconductor.org:包/ geneXtendeR
包短Url	//www.anjoumacpherson.com/packages/geneXtendeR/
包下载报告	下载数据