Tool: clusterProfiler: an R package for comparing biological themes among gene clusters
12
gravatar for Guangchuang Yu
3.0 years ago by
Guangchuang Yu2.2k
China/Guangzhou/Southern Medical University
Guangchuang Yu2.2k wrote:

The clusterProfiler package implements methods to analyze and visualize functional profiles of genomic coordinates (supported by ChIPseeker), gene and gene clusters.

Homepage: https://guangchuangyu.github.io/software/clusterProfiler/

Documentation:https://guangchuangyu.github.io/software/clusterProfiler/documentation/

Issue/Question:https://guangchuangyu.github.io/software/clusterProfiler/#feedback

Citation

Yu G, Wang L, Han Y and He Q*. 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

Overview

Supported ontologies/pathways

Visualization

  • barplot
  • cnetplot
  • dotplot
  • enrichMap
  • gseaplot
  • plotGOgraph (via topGO package)
  • upsetplot

Useful utilities:

  • bitr (Biological Id TranslatoR)
  • compareCluster (biological theme comparison)
  • dropGO (screen out GO term of specific level or specific term)
  • go2ont (convert GO ID to Ontology)
  • go2term (convert GO ID to descriptive term)
  • gofilter (restrict result at specific GO level)
  • gsfilter (restrict result by gene set size)
  • simplify (remove redundant GO terms, supported via GOSemSim)
go gsea R clusterprofiler kegg tool • 3.4k views
ADD COMMENTlink modified 11 months ago • written 3.0 years ago by Guangchuang Yu2.2k
1
gravatar for pshubhamoy
13 months ago by
pshubhamoy20
pshubhamoy20 wrote:

where do I get the code for gseaplot? I would like to change the font size of GSEA plot is there a way to do it with existing package?

ADD COMMENTlink written 13 months ago by pshubhamoy20
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