geneXtendeR

DOI:10.18129 / B9.bioc.geneXtendeR

此包适用于Bioconductor 3.10版本;有关稳定的最新发布版本，请参见geneXtendeR．

优化的ChIP-seq数据功能注释

Bioconductor版本:3.10

geneXtendeR通过探索ChIP-seq峰集注释到变长基因体的相对差异，优化了ChIP-seq峰的功能注释。与之前的技术相比，geneXtendeR只考虑最接近的基因之外的峰值注释，允许用户查看最接近的基因、第二近的基因……的峰值汇总统计信息。，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:Bohdan Khomtchouk [aut, cre]， William Koehler [aut]

维护者:Bohdan Khomtchouk

安装

要安装这个包，启动R(版本“3.6”)并输入:

如果(!requireNamespace("BiocManager"， quiet = TRUE) install.packages("BiocManager") BiocManager::install("geneXtendeR")

对于R的旧版本，请参考相应的Bioconductor释放．

文档

要查看系统中安装的此包版本的文档，请启动R并输入:

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	1.12.0
在Bioconductor	BioC 3.4 (R-3.3)(3.5年)
许可证	GPL (>= 3)
取决于	rtracklayer，GO.db， r (>= 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
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包档案

遵循bob 体育网址 在R会话中使用此包的说明。

源包	geneXtendeR_1.12.0.tar.gz
Windows二进制	geneXtendeR_1.12.0.zip
Mac OS X 10.11 (El Capitan)	geneXtendeR_1.12.0.tgz
源库	git克隆https://git.bioconductor.org/packages/geneXtendeR
源存储库(开发人员访问)	git克隆git@git.bioconductor.org:packages/geneXtendeR
包短Url	//www.anjoumacpherson.com/packages/geneXtendeR/
软件包下载报告	下载数据