clusterProfiler模式物种的GO与KEGG功能富集与注释

支持的20个模式物种列表如下：

Package	Maintainer	Title	Index
org.Hs.eg.db	Bioconductor Package Maintainer	Genome wide annotation for Human	3
org.Mm.eg.db	Bioconductor Package Maintainer	Genome wide annotation for Mouse	5
org.Rn.eg.db	Bioconductor Package Maintainer	Genome wide annotation for Rat	19
org.Sc.sgd.db	Bioconductor Package Maintainer	Genome wide annotation for Yeast	28
org.Dm.eg.db	Bioconductor Package Maintainer	Genome wide annotation for Fly	31
org.At.tair.db	Bioconductor Package Maintainer	Genome wide annotation for Arabidopsis	32
org.Dr.eg.db	Bioconductor Package Maintainer	Genome wide annotation for Zebrafish	37
org.Ce.eg.db	Bioconductor Package Maintainer	Genome wide annotation for Worm	44
org.Bt.eg.db	Bioconductor Package Maintainer	Genome wide annotation for Bovine	53
org.Gg.eg.db	Bioconductor Package Maintainer	Genome wide annotation for Chicken	56
org.Cf.eg.db	Bioconductor Package Maintainer	Genome wide annotation for Canine	61
org.Ss.eg.db	Bioconductor Package Maintainer	Genome wide annotation for Pig	64
org.Mmu.eg.db	Bioconductor Package Maintainer	Genome wide annotation for Rhesus	70
org.EcK12.eg.db	Bioconductor Package Maintainer	Genome wide annotation for E coli strain K12	76
org.Xl.eg.db	Bioconductor Package Maintainer	Genome wide annotation for Xenopus	111
org.Ag.eg.db	Bioconductor Package Maintainer	Genome wide annotation for Anopheles	114
org.Pt.eg.db	Bioconductor Package Maintainer	Genome wide annotation for Chimp	121
org.Pf.plasmo.db	Bioconductor Package Maintainer	Genome wide annotation for Malaria	132
org.EcSakai.eg.db	Bioconductor Package Maintainer	Genome wide annotation for E coli strain Sakai	137
org.Mxanthus.db	Eduardo Illueca Fernández	Genome wide annotation for Myxococcus xanthus DK 1622	944

简单总结clusterProfiler包进行GO、KEGG的富集分析方法，结果输出及内置的图形展示。

#安装富集分析需要的包
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("enrichplot")
BiocManager::install("GSEABase")
BiocManager::install("pathview")
BiocManager::install("clusterProfiler")
#20个模式物种注释文件：https://www.omicsclass.com/article/1244
BiocManager::install("org.Hs.eg.db")
#非模式物种需要的包
BiocManager::install("AnnotationHub")
BiocManager::install("biomaRt")

#######加载必要的包#####################################################
library(clusterProfiler)
library(pathview)
library(GSEABase)
library(enrichplot)
#模式物种
library(AnnotationHub)
library(biomaRt)
############################################################

发表于 2020-04-28 12:50
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分类：R

clusterProfiler模式物种的GO与KEGG功能富集与注释

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