What are the GO and KEGG functions of clusterProfiler
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The list of 20 supported model species is as follows:
PackageMaintainerTitleIndexorg.Hs.eg.dbBioconductor Package MaintainerGenome wide annotation for Human3org.Mm.eg.dbBioconductor Package MaintainerGenome wide annotation for Mouse5org.Rn.eg.dbBioconductor Package MaintainerGenome wide annotation for Rat19org.Sc.sgd.dbBioconductor Package MaintainerGenome wide annotation for Yeast28org.Dm.eg.dbBioconductor Package MaintainerGenome wide annotation for Fly31org.At.tair.dbBioconductor Package MaintainerGenome wide annotation for Arabidopsis32org.Dr.eg.dbBioconductor Package MaintainerGenome wide annotation for Zebrafish37org.Ce.eg.dbBioconductor Package MaintainerGenome wide annotation for Worm44org.Bt.eg.dbBioconductor Package MaintainerGenome wide annotation for Bovine53org.Gg.eg.dbBioconductor Package MaintainerGenome wide annotation for Chicken56org.Cf.eg.dbBioconductor Package MaintainerGenome wide annotation for Canine61org.Ss.eg.dbBioconductor Package MaintainerGenome wide annotation for Pig64org.Mmu.eg.dbBioconductor Package MaintainerGenome wide annotation for Rhesus70org.EcK12.eg.dbBioconductor Package MaintainerGenome wide annotation for E coli strain K1276org.Xl.eg.dbBioconductor Package MaintainerGenome wide annotation for Xenopus111org.Ag.eg.dbBioconductor Package MaintainerGenome wide annotation for Anopheles114org.Pt.eg.dbBioconductor Package MaintainerGenome wide annotation for Chimp121org.Pf.plasmo.dbBioconductor Package MaintainerGenome wide annotation for Malaria132org.EcSakai.eg.dbBioconductor Package MaintainerGenome wide annotation for E coli strain Sakai137org.Mxanthus.dbEduardo Illueca Fern á ndezGenome wide annotation for Myxococcus xanthus DK 1622944
This paper briefly summarizes the enrichment analysis methods of GO and KEGG in clusterProfiler package, the output of the results and the built-in graphic display.
# install the package if (! requireNamespace ("BiocManager") required for enrichment analysis Quietly = TRUE) install.packages ("BiocManager") BiocManager::install ("enrichplot") BiocManager::install ("GSEABase") BiocManager::install ("pathview") BiocManager::install ("clusterProfiler") # 20 model species annotation files: packages BiocManager::install ("AnnotationHub") BiocManager::install ("biomaRt") # required by https://www..com/article/1244BiocManager::install("org.Hs.eg.db")# non-model species # load necessary packages # library (clusterProfiler) library (pathview) library (GSEABase) library (enrichplot) # pattern species library (AnnotationHub) library (biomaRt) # # # # the above is about the article "what are the GO and KEGG functions of clusterProfiler"? I believe we all have a certain understanding. I hope the content shared by the editor will be helpful to you. If you want to know more about the relevant knowledge, please pay attention to the industry information channel.
