clusterProfiler statistics

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Citations per year

Number of citations per year for the bioinformatics software tool clusterProfiler
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Tool usage distribution map

This map represents all the scientific publications referring to clusterProfiler per scientific context
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Associated diseases

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Popular tool citations

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Protocols

clusterProfiler specifications

Information


Unique identifier OMICS_13440
Name clusterProfiler
Alternative name cluster Profiler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 3.8.1
Stability Stable
Requirements
qvalue, AnnotationDbi, methods, stats, KEGG.db, plyr, utils, testthat, ggplot2, knitr, GO.db, org.Hs.eg.db, AnnotationHub, GOSemSim, GSEABase, tidyr, magrittr, R(>=3.4.0), ReactomePA, prettydoc, pathview, DOSE(>=3.5.1), enrichplot(>=0.99.7), rvcheck
Maintained Yes

Taxon


  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Subtools


  • enrichGO
  • enrichKEGG
  • groupGO

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Guangchuang Yu

Publications for clusterProfiler

clusterProfiler citations

 (211)
call_split

A Five microRNA Signature for Survival Prognosis in Pancreatic Adenocarcinoma based on TCGA Data

2018
Sci Rep
PMCID: 5955976
PMID: 29769534
DOI: 10.1038/s41598-018-22493-5
call_split See protocol

[…] functional annotation enrichment analysis. In the KEGG pathways analysis, enriched pathways were identified according to the hypergeometric distribution with a p-value < 0.05, and were performed with clusterProfiler package. In addition, to provide a readable graphic representation of the complex relationship between target genes and relative KEGG pathway, the “pathway-gene network” was constructe […]

call_split

The extent of liver injury determines hepatocyte fate toward senescence or cancer

2018
PMCID: 5951829
PMID: 29760381
DOI: 10.1038/s41419-018-0622-x
call_split See protocol

[…] es. A corrected P-value < 0.05 was adopted as the standard for judging statistically significant enrichment of cluster genes. KEGG enrichment analysis of different cluster genes was implemented using clusterProfiler R package, and the cutoff for P-value was set at 0.05. Raw sequencing data is publically available at NCBI (GEO accession number GSE108328). […]

call_split

Glycine N methyltransferase inhibits aristolochic acid nephropathy by increasing CYP3A44 and decreasing NQO1 expression in female mouse hepatocytes

2018
Sci Rep
PMCID: 5934382
PMID: 29725048
DOI: 10.1038/s41598-018-22298-6
call_split See protocol

[…] urePrint G3 Mouse GE 8 × 60 K Microarray kit (Agilent Technologies, CA, USA). Genes that were significantly up- or downregulated by more than 2-fold were subjected to GO enrichment analysis using the cluster Profiler software. Normalized intensities were transformed to gene expression log2 ratios between the control and AAI treatment groups. The genes with log2 ratio ≥ 1 or  ≤ −1 and p-value < 0.0 […]

library_books

Comparisons of gene coexpression network modules in breast cancer and ovarian cancer

2018
BMC Syst Biol
PMCID: 5907153
PMID: 29671401
DOI: 10.1186/s12918-018-0530-9

[…] een the two diseases, we also did Gene Set Enrichment Analysis (GSEA) []. GSEA was also done for the three types of enrichment analysis: GO, KEGG, and DO. We implemented the enrichment analysis with ‘clusterProfiler’ []. For all the cases, we let the cutoff be the Benjamini-Hochberg adjusted p-value 0.05, and recorded all the enriched terms with p-value less than 0.05. […]

call_split

Environment dependent striatal gene expression in the BACHD rat model for Huntington disease

2018
Sci Rep
PMCID: 5895842
PMID: 29643462
DOI: 10.1038/s41598-018-24243-z
call_split See protocol

[…] ClusterProfiler (v3.4.4) was employed to identify overrepresented Gene Ontology terms and associated cellular functions in sets of differentially expressed genes (DEGs). Terms with at least three anno […]

library_books

ANLN functions as a key candidate gene in cervical cancer as determined by integrated bioinformatic analysis

2018
PMCID: 5896649
PMID: 29670400
DOI: 10.2147/CMAR.S162813

[…] yzed using the limma package with standard data processing and Gene Ontology (GO) term enrichment analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was developed using the clusterprofiler package., The protein–protein interaction (PPI) network was then executed on the STRING website and Cytoscape software. Subsequently, Weighted Correlation Network Analysis (WGCNA) was […]


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clusterProfiler 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
clusterProfiler 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).

clusterProfiler review

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Thyago

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Desktop
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.