YuLab-SMU/clusterProfiler

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:bar_chart: A universal enrichment tool for interpreting omics data

Stars: 1.2k
Forks: 267
Open beginner issues: 0
Indexed issues: 360

Dominant language: R
License: No license data
Last GitHub push: Aug 14, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
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PR merge metrics: No merged PRs in 30d

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360 open issues indexed

enrichKEGG(organism = "cpd") fails with HTTP 400 after KEGG REST API update Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

YuLab-SMU/clusterProfiler#828 · Opened Sep 14, 2026
Proper GSEA for multi-gene orthogroups/families Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#827 · Opened Sep 9, 2026
enrichKEGG报错，无法连接使用 Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

YuLab-SMU/clusterProfiler#825 · 3 comments · Opened Aug 8, 2026
Error using custom org.db without ENTREZID keytype Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

YuLab-SMU/clusterProfiler#823 · 2 comments · 1 reaction · Opened Jun 30, 2026
Big differences in enricher results between clusterProfiler 4.16.0 and clusterProfiler 4.20.0 Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

YuLab-SMU/clusterProfiler#819 · 6 comments · Opened May 14, 2026
groupGO函数运行失败 Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

YuLab-SMU/clusterProfiler#815 · 1 comment · Opened Apr 3, 2026
The items in "qvalue" column by enrichKEGG （enrichGO-BP-CC-MF） are all "NA" Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#807 · 3 comments · Opened Jan 23, 2026
cnetplot() error: enrichResult subset with grepl fails when color_edge="category" Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

YuLab-SMU/clusterProfiler#802 · 1 comment · Opened Jan 4, 2026
Has this plot been removed in the latest version of the R package? Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#799 · 2 comments · Opened Dec 9, 2025
Error in emapplot_internal(x, showCategory = showCategory, ...) : Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

YuLab-SMU/clusterProfiler#795 · 1 comment · Opened Dec 5, 2025
cex_label_gene not working on v4.14.0 Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

YuLab-SMU/clusterProfiler#794 · 1 comment · Opened Dec 4, 2025
Add GO term level information to enrichment results Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

YuLab-SMU/clusterProfiler#793 · Opened Dec 3, 2025
add ont argument to enricher Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

YuLab-SMU/clusterProfiler#791 · 8 comments · Opened Nov 8, 2025
Why does enrichKEGG() output include Category / Subcategory, but in my case gseKEGG() does not? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#787 · 1 comment · Opened Oct 8, 2025
log-10 transformation introduced infinite values Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#785 · 8 comments · Opened Aug 30, 2025
4.16 bioconductor-clusterprofiler NOT available in https://anaconda.org/ Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

YuLab-SMU/clusterProfiler#784 · 1 comment · Opened Aug 27, 2025
Why doesn’t enrichKEGG() support the readable = TRUE parameter like enrichGO()? Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

YuLab-SMU/clusterProfiler#782 · 2 comments · Opened Jul 22, 2025
enrichGO results not filtered by default pvalueCutoff Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

YuLab-SMU/clusterProfiler#777 · 2 comments · Opened Jun 25, 2025
ont = "ALL" not working in the enrichGO() Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

YuLab-SMU/clusterProfiler#775 · 4 comments · 1 reaction · Opened Jun 5, 2025
Color scales in the new version cannot be easily manipulated Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

YuLab-SMU/clusterProfiler#773 · 1 comment · Opened May 16, 2025
goplot does not find ontology Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

YuLab-SMU/clusterProfiler#771 · 2 comments · Opened May 14, 2025
cannot return enrichKEGG results with compareCluster Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

YuLab-SMU/clusterProfiler#770 · 2 comments · Opened May 8, 2025
Cannot insert dotplot SVGs into Word or PowerPoint for macOS Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

YuLab-SMU/clusterProfiler#769 · 4 comments · Opened May 5, 2025
Unable to specfify ont = "BP" with compareCluster Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

YuLab-SMU/clusterProfiler#767 · 1 comment · Opened Apr 24, 2025
Differences in gseGO and compareCluster (clusterProfiler) results Open

Difficulty 4/5 3-5 days Newbie friendliness 32/100

YuLab-SMU/clusterProfiler#763 · 2 comments · Opened Mar 26, 2025
i am receiving the following error with enrichkegg Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#759 · 7 comments · Opened Feb 20, 2025
cnetplot() in the latest clusterProfiler, v4.14.4, does not work correctly Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

YuLab-SMU/clusterProfiler#758 · 6 comments · Opened Feb 20, 2025
Unable to Install clusterprofiler on R v4.4.2 Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#757 · 1 comment · Opened Feb 19, 2025
Comparecluster analysis is not working for me with same data Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

YuLab-SMU/clusterProfiler#754 · 7 comments · Opened Jan 20, 2025
`simplify` for output from `clusterProfiler::GSEA`? Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

YuLab-SMU/clusterProfiler#753 · 3 comments · 1 reaction · Opened Jan 20, 2025
Meaning of compareClusterResults Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#752 · 1 comment · Opened Jan 15, 2025
Achieve COG/KOG enrichment analysis using clusterProfiler Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#751 · 1 comment · Opened Jan 13, 2025
Feature Request: Sign Test Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#750 · 1 reaction · Opened Jan 8, 2025
Question about the result of GO:BP analysis: only one or two gene related to one GO term Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#749 · 1 comment · Opened Dec 26, 2024
Can't update package to 4.12.6 Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

YuLab-SMU/clusterProfiler#746 · 1 comment · Opened Dec 2, 2024
feature request: LLM generated gene sets Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#745 · Opened Nov 27, 2024
Unable to Convert Pathway ID to Gene Set Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

YuLab-SMU/clusterProfiler#743 · Opened Nov 21, 2024
enrichKEGG issue：the Description column and ID information are identical in 4.10.0 Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

YuLab-SMU/clusterProfiler#742 · 2 comments · Opened Nov 19, 2024
how to install clusterProfiler 4.2.2 version? Open

Difficulty 1/5 Under an hour Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#740 · 2 comments · Opened Nov 11, 2024
smth wrong with enrichGO Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

YuLab-SMU/clusterProfiler#737 · 1 comment · Opened Oct 30, 2024
Meta-analysis Functionality is Not Available Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#734 · Opened Oct 22, 2024
Mitochondrial Genes and Annotations missing from EnrichGO Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#733 · 4 comments · Opened Oct 21, 2024
How to run enrichment analysis of metabolites using clusterProfier Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#731 · 5 comments · Opened Oct 15, 2024
how to compare different conditions Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

YuLab-SMU/clusterProfiler#730 · Opened Sep 30, 2024
enrichWP is not working for a few organisms Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

YuLab-SMU/clusterProfiler#729 · 3 comments · Opened Sep 30, 2024
gofilter function ERROR: object 'topNode' not found Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#728 · 1 comment · Opened Sep 29, 2024
Error: unable to open database file Traceback: Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

YuLab-SMU/clusterProfiler#727 · 1 comment · Opened Sep 27, 2024
clusterProfiler: BgRatio N value does not equal set gene universe size Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#723 · 1 comment · Opened Sep 13, 2024
using compareCluster to compare gene sets from different species Open

Difficulty 1/5 Under an hour Newbie friendliness 25/100

YuLab-SMU/clusterProfiler#722 · 1 comment · Opened Sep 13, 2024
problem with gseGO() Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

YuLab-SMU/clusterProfiler#721 · 1 comment · Opened Aug 31, 2024

YuLab-SMU/clusterProfiler

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