statistical analysis and visulization of functional profiles for genes and gene clusters

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Documentation for package ‘clusterProfiler’ version 2.0.1

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clusterProfiler-package statistical analysis and visulization of functional profiles for genes and gene clusters The package implements methods to analyze and visualize functional profiles of gene and gene clusters.
buildGOmap buildGOmap
clusterProfiler statistical analysis and visulization of functional profiles for genes and gene clusters The package implements methods to analyze and visualize functional profiles of gene and gene clusters.
cnetplot cnetplot
compareCluster Compare gene clusters functional profile Given a list of gene set, this function will compute profiles of each gene cluster.
compareClusterResult-class Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
DataSet Datasets gcSample contains a sample of gene clusters.
enrichGO GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories with FDR control.
enrichKEGG KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control.
enrichMap enrichMap
gcSample Datasets gcSample contains a sample of gene clusters.
getGeneSet.BP getGeneSet.BP
getGeneSet.CC getGeneSet.CC
getGeneSet.GO getGeneSet.GO
getGeneSet.KEGG getGeneSet.KEGG
getGeneSet.MF getGeneSet.MF
getGOLevel get GOIDs at a specific level
Gff2GeneTable Gff2GeneTable
groupGO Functional Profile of a gene set at specific GO level. Given a vector of genes, this function will return the GO profile at specific level.
groupGOResult-class Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level.
gseaplot gseaplot
gseGO gseGO
gseKEGG gseKEGG
plot plot method
plot-method Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
plot-method plot method
plotting.clusterProfile plotting-clusterProfile
show-method Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
show-method Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level.
summary-method Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
viewKEGG viewKEGG function is for visualize KEGG pathways works with enrichResult object to visualize enriched KEGG pathway