这个包是3.14版本Bioconductor;的稳定,最新的发布版本,请参阅geneXtendeR。
Bioconductor版本:3.14
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 >
从内部引用(R,回车引用(“geneXtendeR”)
):
安装这个包,开始R(版本“4.1”)并输入:
如果(!要求(“BiocManager”,悄悄地= TRUE)) install.packages (“BiocManager”) BiocManager::安装(“geneXtendeR”)
R的旧版本,请参考适当的Bioconductor释放。
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”)
geneXtendeR.pdf | ||
参考手册 |
biocViews | 注释,ChIPSeq,ChipOnChip,报道,DataImport,DifferentialPeakCalling,去,遗传学,GenomeAnnotation,HistoneModification,NaturalLanguageProcessing,PeakDetection,软件,可视化 |
版本 | 1.20.0 |
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 |
遵循bob 体育网址 指示在R会话中使用这个包。
源包 | geneXtendeR_1.20.0.tar.gz |
Windows二进制 | geneXtendeR_1.20.0.zip |
macOS 10.13(高山脉) | geneXtendeR_1.20.0.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 |