clusterProfiler protocols

View clusterProfiler computational protocol

clusterProfiler statistics

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Associated diseases

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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

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Versioning


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Documentation


Maintainer


  • person_outline Guangchuang Yu <>

Publications for clusterProfiler

clusterProfiler in pipelines

 (9)
2018
PMCID: 5821079
PMID: 29463655
DOI: 10.1128/mBio.01650-17

[…] for each gene and condition. the optimal number of clusters was defined using the elbow plot method and circular heatmaps drawn using circos (). go enrichment analysis was carried out with the enrichgo function in the r package clusterprofiler version 3.4.4 () by the molecular function ontology method and the holm method to correct p values for multiple comparisons. categories […]

2017
PMCID: 5499869
PMID: 28379492
DOI: 10.1093/nar/gkx235

[…] fold change (>1) and the correspondent statistical significance (p-value < 0.05). functional annotation enrichment analysis with gene ontology terms and kegg pathways were performed using the clusterprofiler bioconductor package. in order to perform motif analysis, transcript sequences were retrieved from gencode 22. control sequences for motif analysis were generated by selecting […]

2017
PMCID: 5508029
PMID: 28751903
DOI: 10.3389/fpls.2017.01217

[…] al., ) was used to remove redundancy from the enriched go terms and produced a summary. the identification of enriched pathways in arabidopsis gene sets was performed with the bioconductor r package clusterprofiler (yu et al., ). the enrichkegg function was used with bejamin-hochberg as p-value correction method for the multiple testing and a q-value cutoff of 0.05., gene co-expression […]

2017
PMCID: 5587750
PMID: 28549158
DOI: 10.1093/nar/gkx475

[…] into active, bivalent and other states using the intensities of histone modifications around tss using chip-seq data of wt mescs. then, gene ontology analysis in each cluster was performed with clusterprofiler ()., to compare the intensities of chip-seq signals between different chip samples prepared from different inputs, we performed between-sample normalization. first, means of counts […]

2017
PMCID: 5664118
PMID: 29027943
DOI: 10.3390/genes8100268

[…] from r software., during functional enrichment analysis of genes, the online software database for annotation, visualization, and integrated discovery (david 6.8, https://david.ncifcrf.gov/), clusterprofiler package and signaling pathway impact analysis (spia) package of r were utilized to perform gene ontology (go) analysis and kyoto encyclopedia of genes and genomes (kegg) pathway […]


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clusterProfiler in publications

 (191)
PMCID: 5955976
PMID: 29769534
DOI: 10.1038/s41598-018-22493-5

[…] 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” […]

PMCID: 5951829
PMID: 29760381
DOI: 10.1038/s41419-018-0622-x

[…] 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)., all data are presented as mean ± standard […]

PMCID: 5934382
PMID: 29725048
DOI: 10.1038/s41598-018-22298-6

[…] 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 <  […]

PMCID: 5907153
PMID: 29671401
DOI: 10.1186/s12918-018-0530-9

[…] 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., we did module […]

PMCID: 5895842
PMID: 29643462
DOI: 10.1038/s41598-018-24243-z

[…] derived from salmon (v0.7.2) when determining transcript-level compositions of individual genes. transcript-level differential expression was further explored and verified with kallisto (v0.43.0)., 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 […]


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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.