Issues

• Proper GSEA for multi-gene orthogroups/families

  YuLab-SMU/clusterProfiler#827 · Filter by author desmodus1984 opened on Sep 9, 2026

• groupGO函数运行失败

  YuLab-SMU/clusterProfiler#815 · Filter by author jiangzhichao47-create opened on Apr 3, 2026
  1

• Why does enrichKEGG() output include Category / Subcategory, but in my case gseKEGG() does not?

  YuLab-SMU/clusterProfiler#787 · Filter by author laleoarrow opened on Oct 8, 2025
  1

• 4.16 bioconductor-clusterprofiler NOT available in https://anaconda.org/

  YuLab-SMU/clusterProfiler#784 · Filter by author ray1919 opened on Aug 27, 2025
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• Why doesn’t enrichKEGG() support the readable = TRUE parameter like enrichGO()?

  YuLab-SMU/clusterProfiler#782 · Filter by author Wang-Ande opened on Jul 22, 2025
  2

• enrichGO results not filtered by default pvalueCutoff

  YuLab-SMU/clusterProfiler#777 · Filter by author jtourig opened on Jun 25, 2025
  2

• Color scales in the new version cannot be easily manipulated

  YuLab-SMU/clusterProfiler#773 · Filter by author zuzkamat opened on May 16, 2025
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• cannot return enrichKEGG results with compareCluster

  YuLab-SMU/clusterProfiler#770 · Filter by author kristina-sakers opened on May 8, 2025
  2

• Cannot insert dotplot SVGs into Word or PowerPoint for macOS

  YuLab-SMU/clusterProfiler#769 · Filter by author nehawali21 opened on May 5, 2025
  4

• Unable to specfify ont = "BP" with compareCluster

  YuLab-SMU/clusterProfiler#767 · Filter by author CarrieMeeksPatience opened on Apr 24, 2025
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• Differences in gseGO and compareCluster (clusterProfiler) results

  YuLab-SMU/clusterProfiler#763 · Filter by author acebollada80 opened on Mar 26, 2025
  2

• i am receiving the following error with enrichkegg

  YuLab-SMU/clusterProfiler#759 · Filter by author vinodkumarvalluri opened on Feb 20, 2025
  7

• Comparecluster analysis is not working for me with same data

  YuLab-SMU/clusterProfiler#754 · Filter by author Sidragull57 opened on Jan 20, 2025
  7

• Feature Request: Sign Test

  YuLab-SMU/clusterProfiler#750 · Filter by author DarioS opened on Jan 8, 2025
  1

• Question about the result of GO:BP analysis: only one or two gene related to one GO term

  YuLab-SMU/clusterProfiler#749 · Filter by author Mancang-Yu opened on Dec 26, 2024
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• feature request: LLM generated gene sets

  YuLab-SMU/clusterProfiler#745 · Filter by author zia1138 opened on Nov 27, 2024

• Unable to Convert Pathway ID to Gene Set

  YuLab-SMU/clusterProfiler#743 · Filter by author DarioS opened on Nov 21, 2024

• Mitochondrial Genes and Annotations missing from EnrichGO

  YuLab-SMU/clusterProfiler#733 · Filter by author Dragonmasterx87 opened on Oct 21, 2024
  4

• How to run enrichment analysis of metabolites using clusterProfier

  YuLab-SMU/clusterProfiler#731 · Filter by author Krithika-Bhuvan opened on Oct 15, 2024
  5

• how to compare different conditions

  YuLab-SMU/clusterProfiler#730 · Filter by author Flu09 opened on Sep 30, 2024

• Error: unable to open database file Traceback:

  YuLab-SMU/clusterProfiler#727 · Filter by author jmzhang1911 opened on Sep 27, 2024
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• clusterProfiler: BgRatio N value does not equal set gene universe size

  YuLab-SMU/clusterProfiler#723 · Filter by author fafaris39 opened on Sep 13, 2024
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• using compareCluster to compare gene sets from different species

  YuLab-SMU/clusterProfiler#722 · Filter by author lanasushko opened on Sep 13, 2024
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• problem with gseGO()

  YuLab-SMU/clusterProfiler#721 · Filter by author Flu09 opened on Aug 31, 2024
  1

• RStudio is crashing when running compareCluster

  YuLab-SMU/clusterProfiler#719 · Filter by author nfancy opened on Aug 22, 2024
  1