Body: <p>With <a href="https://huttenhower.sph.harvard.edu/humann" rel="nofollow noreferrer">HUMAnN3</a>, I got the result of the KEGG KO annotation (by <em>humann_regroup_table</em>:humann_regroup_table --input hmp_subset_genefamilies.tsv --groups uniref90_ko --output hmp_subset_genefamilies_uniref90_ko.tsv).</p>
  <p>I need to quantify/transform the KEGG KO annotation to KEGG module definitions.</p>
  <p>However, I did not find the relevant guidance/instruction. Are there any relevant tutorials available for reference?</p>
  <p>Just like the packages (&quot;clusterProfiler&quot;) using R for transform to KEGG pathway (KEGG pathway enrichment analysis).</p>
  <p>Thanks a lot!</p>
  <p>Any help will get me out of trouble!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-29T12:36:03.370Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-06T12:06:39.573Z
Comments.Text: The problem with the question is it's not clear what "quantify/transform" KEGG really means. Nor is it clear what your background in coding or SQL is because this is a fairly simple operation. Sure I've done loads of this, but whether that transferable here its difficult to assess.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-09T02:54:23.903Z
Comments.Text: @M__  Thank you for replying. "quantify/transform" KEGG means that the result of the KEGG KO annotation (genome information) is mapped to KEGG modules for the functional annotation like "KEGG Pathway Enrichment Analysis" (by R package: clusterProfiler). I'm just starting to learn these. Can you give me some advice? Thanks a lot.
Comments.UserDisplayName: Xin Xu
Tags: <clustering><pathway><kegg>
Title: How to obtain the KEGG mudule based on KEGG KO? (KEGG mudule enrichment)
ThreadText: # How to obtain the KEGG mudule based on KEGG KO? (KEGG mudule enrichment)
  
  (Asked by: username_0 on 2023-09-29)
  
  With [HUMAnN3](https://huttenhower.sph.harvard.edu/humann), I got the result of the KEGG KO annotation (by *humann\_regroup\_table*:humann\_regroup\_table --input hmp\_subset\_genefamilies.tsv --groups uniref90\_ko --output hmp\_subset\_genefamilies\_uniref90\_ko.tsv).
  
  I need to quantify/transform the KEGG KO annotation to KEGG module definitions.
  
  However, I did not find the relevant guidance/instruction. Are there any relevant tutorials available for reference?
  
  Just like the packages ("clusterProfiler") using R for transform to KEGG pathway (KEGG pathway enrichment analysis).
  
  Thanks a lot!
  
  Any help will get me out of trouble!
  
  **Tags:** clustering, pathway, kegg
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: The problem with the question is it's not clear what "quantify/transform" KEGG really means. Nor is it clear what your background in coding or SQL is because this is a fairly simple operation. Sure I've done loads of this, but whether that transferable here its difficult to assess.  
  > **username_0**: @username_2  Thank you for replying. "quantify/transform" KEGG means that the result of the KEGG KO annotation (genome information) is mapped to KEGG modules for the functional annotation like "KEGG Pathway Enrichment Analysis" (by R package: clusterProfiler). I'm just starting to learn these. Can you give me some advice? Thanks a lot.  
  
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