clusterProfiler模式物种的GO与KEGG功能富集与注释

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:

PackageMaintainerTitleIndex
org.Hs.eg.dbBioconductor Package MaintainerGenome wide annotation for Human3
org.Mm.eg.dbBioconductor Package MaintainerGenome wide annotation for Mouse5
org.Rn.eg.dbBioconductor Package MaintainerGenome wide annotation for Rat19
org.Sc.sgd.dbBioconductor Package MaintainerGenome wide annotation for Yeast28
org.Dm.eg.dbBioconductor Package MaintainerGenome wide annotation for Fly31
org.At.tair.dbBioconductor Package MaintainerGenome wide annotation for Arabidopsis32
org.Dr.eg.dbBioconductor Package MaintainerGenome wide annotation for Zebrafish37
org.Ce.eg.dbBioconductor Package MaintainerGenome wide annotation for Worm44
org.Bt.eg.dbBioconductor Package MaintainerGenome wide annotation for Bovine53
org.Gg.eg.dbBioconductor Package MaintainerGenome wide annotation for Chicken56
org.Cf.eg.dbBioconductor Package MaintainerGenome wide annotation for Canine61
org.Ss.eg.dbBioconductor Package MaintainerGenome wide annotation for Pig64
org.Mmu.eg.dbBioconductor Package MaintainerGenome wide annotation for Rhesus70
org.EcK12.eg.dbBioconductor Package MaintainerGenome wide annotation for E coli strain K1276
org.Xl.eg.dbBioconductor Package MaintainerGenome wide annotation for Xenopus111
org.Ag.eg.dbBioconductor Package MaintainerGenome wide annotation for Anopheles114
org.Pt.eg.dbBioconductor Package MaintainerGenome wide annotation for Chimp121
org.Pf.plasmo.dbBioconductor Package MaintainerGenome wide annotation for Malaria132
org.EcSakai.eg.dbBioconductor Package MaintainerGenome wide annotation for E coli strain Sakai137
org.Mxanthus.dbEduardo Illueca FernándezGenome wide annotation for Myxococcus xanthus DK 1622944


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

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