Issues

• Proper GSEA for multi-gene orthogroups/families

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

• 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
  1

• clusterProfiler: BgRatio N value does not equal set gene universe size

  YuLab-SMU/clusterProfiler#723 · Filter by author fafaris39 opened on Sep 13, 2024
  1

• using compareCluster to compare gene sets from different species

  YuLab-SMU/clusterProfiler#722 · Filter by author lanasushko opened on Sep 13, 2024
  1

• problem with gseGO()

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

• ridgePlot Axis Ticks Spacing is Sometimes Insufficient

  YuLab-SMU/clusterProfiler#716 · Filter by author DarioS opened on Aug 19, 2024
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• KEGG analysis of metabolites

  YuLab-SMU/clusterProfiler#712 · Filter by author Echo-ylq opened on Jul 30, 2024
  2

• enrichKegg function, qvalueCutoff not working, getting as well non-significant results

  YuLab-SMU/clusterProfiler#710 · Filter by author nina-hahn opened on Jul 22, 2024
  4

• gseKEGG function running indefinitely with a gene list of over 3000 genes

  YuLab-SMU/clusterProfiler#709 · Filter by author Sophia409 opened on Jul 21, 2024
  1

• No gene can be mapped when using enrichKEGG

  YuLab-SMU/clusterProfiler#708 · Filter by author Yanqiu-T opened on Jul 19, 2024
  11

• "I performed the gseGO function using clusterProfiler for all ontologies together, but I wasn't able to apply the simplify function to remove redundancy. I tried various options suggested online, but none worked. As a workaround, I ran gseGO for each ontology (BP, MF, CC) separately and then removed redundancy for each ontology using GOsim. Is it correct to combine the results from all ontologies into one file and then combining it with metadata from one ontology (e.g., the output of gseGO for BP) to create enrichment plots?" or what could be the easiest way to perfrom that

  YuLab-SMU/clusterProfiler#707 · Filter by author Sidragull57 opened on Jul 16, 2024
  13

• "400 Bad Request" using enrichKEGG function from the clusterProfiler

  YuLab-SMU/clusterProfiler#706 · Filter by author RouaPopescu opened on Jul 15, 2024
  2

• compareCluster GSEA + universal annotation = does not work

  YuLab-SMU/clusterProfiler#705 · Filter by author philousap opened on Jul 11, 2024
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• The GeneRatio denominator does not correspond to the number of input genes.

  YuLab-SMU/clusterProfiler#703 · Filter by author CharlineJnnt opened on Jul 10, 2024
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• gseGO Produces Results Table with Zero Rows

  YuLab-SMU/clusterProfiler#702 · Filter by author DarioS opened on Jul 2, 2024
  2

• User Manual Has Minimal Discussion of Universe Choices

  YuLab-SMU/clusterProfiler#701 · Filter by author DarioS opened on Jul 2, 2024

• [FeatureRequest] color category and gene labels differently in cnetplot

  YuLab-SMU/clusterProfiler#700 · Filter by author wbvguo opened on Jun 28, 2024

• Retrieve the set of genes with assigned GO

  YuLab-SMU/clusterProfiler#698 · Filter by author m-bogaerts opened on Jun 17, 2024
  1

• A strange non-given GO comment appears

  YuLab-SMU/clusterProfiler#697 · Filter by author Chewxway opened on Jun 12, 2024
  8

• Upsetplot is cropped

  YuLab-SMU/clusterProfiler#696 · Filter by author nina-hahn opened on Jun 5, 2024
  4

• gseKEGG using KEGG database error (cannot open URL 'https://rest.kegg.jp/conv/ncbi=geneid/mmu': HTTP status was '400 Bad Request')

  YuLab-SMU/clusterProfiler#694 · Filter by author ChoIYS98 opened on May 17, 2024
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• Perform gseaplot2 using seurat DEG output.

  YuLab-SMU/clusterProfiler#693 · Filter by author synatkeamsk opened on May 9, 2024

• How do I change the width of each coloum in the heatmap in the treeplot?

  YuLab-SMU/clusterProfiler#692 · Filter by author CyrusWang57 opened on May 8, 2024

• All p-values are equal to 1

  YuLab-SMU/clusterProfiler#690 · Filter by author aminakur opened on Apr 22, 2024
  1