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clusterProfiler

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

Authors

Guangchuang YU, School of Public Health, The University of Hong Kong http://ygc.name

Citation

Please cite the following article when using clusterProfiler:

Yu G, Wang L, Han Y and He. Q (2012). 
clusterProfiler: an R package for comparing biological themes among gene clusters.
OMICS: A Journal of Integrative Biology, 16(5), pp. 284-287.

URL: http://online.liebertpub.com/doi/abs/10.1089/omi.2011.0118

License

All source code is copyright, under the Artistic-2.0 License. For more information on Artistic-2.0 License see http://opensource.org/licenses/Artistic-2.0

Installation

To install:

the latest released version: biocLite("clusterProfiler")
the latest development version: install_github(c("DOSE", "clusterProfiler"), "GuangchuangYu")

Find out more at http://www.bioconductor.org/packages/release/bioc/html/clusterProfiler.html and check out the vignette.

Bugs/Feature requests

If you have any, let me know. Thx!

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Version

Version

2.0.1

License

Artistic-2.0

Issues

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Repository

https://github.com/GuangchuangYu/clusterProfiler

Maintainer

Guangchuang Yu

Last Published

February 15th, 2017

Functions in clusterProfiler (2.0.1)

plotting.clusterProfile

plotting-clusterProfile

groupGOResult-class

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

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

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.

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.

compareClusterResult-class

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

Datasets gcSample contains a sample of gene clusters.

get GOIDs at a specific level

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

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

getGeneSet.KEGG

getGeneSet.KEGG

Compare gene clusters functional profile Given a list of gene set, this function will compute profiles of each gene cluster.