<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>

CC BY-SA 4.0
2023-09-29T12:36:03.370Z
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.
Community
CC BY-SA 4.0
2023-10-06T12:06:39.573Z
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.
M__
CC BY-SA 4.0
2023-10-09T02:54:23.903Z
@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.
Xin Xu
<clustering><pathway><kegg>
How to obtain the KEGG mudule based on KEGG KO? (KEGG mudule enrichment)
# 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**: @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.  

---

## 0 answers

