clusterProfiler specifications

Unique identifier:
OMICS_13440
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Alternative name:
cluster Profiler
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
Artistic License version 2.0
Version:
3.6.0
Requirements:
DOSE

Subtools

  • groupGO
  • enrichGO
  • enrichKEGG
  • Animals
    • Homo sapiens
    • Mus musculus
  • Fungi
    • Saccharomyces cerevisiae

versioning

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No versioning.

clusterProfiler distribution

download

clusterProfiler support

Documentation

Maintainer

  • Guangchuang Yu <>

forum

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Credits

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Publications

Institution(s)

State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China

Funding source(s)

This work was supported by National ‘‘973’’ Projects of China (2011CB910700), the 2007 Chang-Jiang Scholars Program, ‘‘211’’ Projects, National Natural Science Foundation of China (20871057), Guangdong Natural Science Research Grant (32209003), and the Fundamental Research Funds for the Central Universities (21611303 and 11610101).

User review

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1 user review

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1 user review

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Thyago

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One of the best packages out there to perform functional analyses (e.g. over-representation, GSEA, bio-theme). It has also pretty ggplot2-based plotting functions to visually communicate your results. In addition, it supports many ontologies/pathways db, such as: Gene Ontology (Amigo), KEGG, DAVID, Reactome, Disease Ontology, Molecular Signature Databases and CUSTOM DBs. In my point of view, plotting functionalities are fast and pretty, especially the clusterprofileR::barplot() and ::dotplot() functions. At last, documentation is example-driven and is more than enough to understand and use the package really quickly. As a final note, the author is very attentive to help beginners in forums and alikes, and the code runs smoothly and fast in non-workstation machines.

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