Package: clusterProfiler 4.13.0

Guangchuang Yu

clusterProfiler: A universal enrichment tool for interpreting omics data

This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources and thus can be applied in diverse scenarios. It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation. Datasets obtained from multiple treatments and time points can be analyzed and compared in a single run, easily revealing functional consensus and differences among distinct conditions.

Authors:Guangchuang Yu [aut, cre, cph], Li-Gen Wang [ctb], Erqiang Hu [ctb], Xiao Luo [ctb], Meijun Chen [ctb], Giovanni Dall'Olio [ctb], Wanqian Wei [ctb], Chun-Hui Gao [ctb]

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clusterProfiler.pdf |clusterProfiler.html✨
clusterProfiler/json (API)
NEWS

# Install 'clusterProfiler' in R:
install.packages('clusterProfiler', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/guangchuangyu/clusterprofiler/issues

Datasets:
  • DE_GSE8057 - Datasets gcSample contains a sample of gene clusters.
  • gcSample - Datasets gcSample contains a sample of gene clusters.
  • kegg_category - Datasets gcSample contains a sample of gene clusters.
  • kegg_species - Datasets gcSample contains a sample of gene clusters.

On BioConductor:clusterProfiler-4.13.0(bioc 3.20)clusterProfiler-4.12.0(bioc 3.19)

bioconductor-package

68 exports 4.97 score 118 dependencies 44 dependents 2.2k mentions

Last updated 2 months agofrom:3dc99f8edf

Exports:%<>%%>%append_kegg_categoryarrangebitrbitr_keggbrowseKEGGbuildGOmapcnetplotcompareClusterdotplotdownload_KEGGdropGOemapplotenrichDAVIDenricherenrichGOenrichKEGGenrichMKEGGenrichPCenrichWPfiltergeneIDgeneInCategoryget_wp_organismsgetPPIgetTaxIDgetTaxInfoGff2GeneTablego2ontgo2termgofiltergoplotgroup_bygroupGOGSEAgseaplotgseGOgseKEGGgseMKEGGgsePCgseWPgsfiltergson_GOgson_KEGGgson_KEGG_mappergson_WPheatplotidTypeko2namemerge_resultmutatenplotGOgraphread.blast2goread.gafread.gmtread.gmt.pcread.gmt.wprenameridgeplotsearch_kegg_organismselectsetReadablesimplifyslicesummariseuniprot_get

Dependencies:AnnotationDbiapeaplotaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdigestDOSEdownloaderdplyrenrichplotfansifarverfastmapfastmatchfgseaformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggraphggrepelggtreeglueGO.dbGOSemSimgraphlayoutsgridExtragridGraphicsgsongtableHDO.dbhttrigraphIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplogrplyrpngpolyclippurrrqvalueR6RColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangRSQLiteS4VectorsscalesscatterpieshadowtextsnowstringistringrsyssystemfontstibbletidygraphtidyrtidyselecttidytreetreeiotweenrUCSC.utilsutf8vctrsviridisviridisLitewithrXVectoryulab.utilszlibbioc

Statistical analysis and visualization of functional profiles for genes and gene clusters

Guangchuang Yu

Rendered fromclusterProfiler.Rmdusingknitr::rmarkdownon Jun 24 2024.

Last update: 2019-12-04
Started: 2015-05-17

Readme and manuals

Help Manual

Help pageTopics
append_kegg_categoryappend_kegg_category
bitrbitr
bitr_keggbitr_kegg
browseKEGGbrowseKEGG
Compare gene clusters functional profilecompareCluster
Datasets gcSample contains a sample of gene clusters.DataSet DE_GSE8057 gcSample kegg_category kegg_species
download_KEGGdownload_KEGG
dropGOdropGO
enrichDAVIDenrichDAVID
enricherenricher
GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.enrichGO
KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control.enrichKEGG
KEGG Module Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG Module categories with FDR control.enrichMKEGG
enrichPCenrichPC
enrichWPenrichWP
get_wp_organismget_wp_organisms
getPPIgetPPI
getTaxIDgetTaxID
getTaxInfogetTaxInfo
Gff2GeneTableGff2GeneTable
go2ontgo2ont
go2termgo2term
gofiltergofilter
Functional Profile of a gene set at specific GO level. Given a vector of genes, this function will return the GO profile at a specific level.groupGO
Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level.groupGOResult-class show,groupGOResult-method
GSEAGSEA
gseGOgseGO
gseKEGGgseKEGG
gseMKEGGgseMKEGG
gsePCgsePC
gseWPgseWP
gson_KEGGgson_GO
gson_KEGGgson_KEGG
Build KEGG annotation for novel species using KEGG Mappergson_KEGG_mapper
gson_WPgson_WP
idTypeidType
ko2nameko2name
merge_resultmerge_result
plotGOgraphplotGOgraph
read.gmt.pcread.gmt.pc
search_kegg_organismsearch_kegg_organism
simplify methodsimplify simplify,compareClusterResult-method simplify,enrichResult-method simplify,gseaResult-method
uniprot_getuniprot_get