---
title: "Statistical analysis and visualization of functional profiles for genes and gene clusters"
author: "Guangchuang Yu\\

        School of Basic Medical Sciences, Southern Medical University"
date: "`r Sys.Date()`"
output:
  prettydoc::html_pretty:
    theme: cayman
    highlight: github
  pdf_document:
    toc: true
vignette: >
  %\VignetteIndexEntry{Statistical analysis and visualization of functional profiles for genes and gene clusters}
  %\VignetteEngine{knitr::rmarkdown}
  %\usepackage[utf8]{inputenc}
  %\VignetteEncoding{UTF-8}
---

```{r style, echo=FALSE, results="asis", message=FALSE}
knitr::opts_chunk$set(tidy = FALSE,
                      warning = FALSE,
                      message = FALSE)
```

# Overview

[clusterProfiler](https://www.bioconductor.org/packages/clusterProfiler) implements methods to analyze and visualize functional profiles of genomic coordinates (supported by [ChIPseeker](https://www.bioconductor.org/packages/ChIPseeker)), gene and gene clusters.

## Supported Analysis

+ Over-Representation Analysis
+ Gene Set Enrichment Analysis
+ Biological theme comparison

## Supported ontologies/pathways

+ Disease Ontology (via [DOSE](https://www.bioconductor.org/packages/DOSE))
+ [Network of Cancer Gene](http://ncg.kcl.ac.uk/) (via [DOSE](https://www.bioconductor.org/packages/DOSE))
+ [DisGeNET](http://www.disgenet.org/web/DisGeNET/menu/home) (via [DOSE](https://www.bioconductor.org/packages/DOSE))
+ Gene Ontology (supports many species with GO annotation query online via [AnnotationHub](https://bioconductor.org/packages/AnnotationHub/))
+ KEGG Pathway and Module with latest online data (supports more than 4000 species listed in <http://www.genome.jp/kegg/catalog/org_list.html>)
+ Reactome Pathway (via [ReactomePA](https://www.bioconductor.org/packages/ReactomePA))
+ DAVID (via [RDAVIDWebService](https://www.bioconductor.org/packages/RDAVIDWebService))
+ [Molecular Signatures Database](http://software.broadinstitute.org/gsea/msigdb)
	* hallmark gene sets
	* positional gene sets
	* curated gene sets
	* motif gene sets
	* computational gene sets
	* GO gene sets
	* oncogenic signatures
	* immunologic signatures
+ Other Annotations
	* from other sources (e.g. [DisGeNET](http://www.disgenet.org/web/DisGeNET/menu/home) as [an example](https://guangchuangyu.github.io/2015/05/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/))
	* user's annotation
	* customized ontology
	* and many others

## Visualization

+ barplot
+ cnetplot
+ dotplot
+ emapplot
+ gseaplot
+ goplot
+ upsetplot

# Vignette


Please go to <https://yulab-smu.github.io/clusterProfiler-book/> for the full vignette.


# Citation

If you use [clusterProfiler](https://www.bioconductor.org/packages/clusterProfiler) in published research, please cite:


__*G Yu*__, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters. **_OMICS: A Journal of Integrative Biology_** 2012, 16(5):284-287. doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)



# Need helps?


If you have questions/issues, please visit
[clusterProfiler homepage](https://guangchuangyu.github.io/software/clusterProfiler/) first.
Your problems are mostly documented. If you think you found a bug, please follow
[the guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/) and
provide a reproducible example to be posted
on
[github issue tracker](https://github.com/GuangchuangYu/clusterProfiler/issues).
For questions, please post
to [Bioconductor support site](https://support.bioconductor.org/) and tag your
post with *clusterProfiler*.


