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clusterProfiler (version 3.0.2)

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

Description

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

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Version

Version

3.0.2

License

Artistic-2.0

Maintainer

Guangchuang Yu

Last Published

February 15th, 2017

Functions in clusterProfiler (3.0.2)

DataSet

Datasets gcSample contains a sample of gene clusters.
download.KEGG

download.KEGG
plotGOgraph

plotGOgraph
bitr_kegg

bitr_kegg
go2ont

go2ont
fortify.compareClusterResult

fortify
go2term

go2term
groupGOResult-class

Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level.
compareClusterResult-class

Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
plotting.clusterProfile

plotting-clusterProfile
buildGOmap

buildGOmap
gseGO

gseGO
enricher

enricher
gseKEGG

gseKEGG
enrichKEGG

KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control.
gseMKEGG

gseMKEGG
merge_result

merge_result
enrichGO

GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control.
gofilter

gofilter
groupGO

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.
simplify

simplify method
dropGO

dropGO
bitr

bitr
enrichDAVID

enrichDAVID
read.gmt

read.gmt
idType

idType
Gff2GeneTable

Gff2GeneTable
dotplot,compareClusterResult-method

dotplot
plot

plot method
getGOLevel

get GOIDs at a specific level
search_kegg_organism

search_kegg_organism
enrichMKEGG

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.
GSEA

GSEA
clusterProfiler-package

statistical analysis and visualization of functional profiles for genes and gene clusters The package implements methods to analyze and visualize functional profiles of gene and gene clusters.
compareCluster

Compare gene clusters functional profile
viewKEGG

viewKEGG function is for visualize KEGG pathways works with enrichResult object to visualize enriched KEGG pathway