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Hi,
The current GO analysis tool used in the RNAseq training is [goseq](https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fgoseq%2Fgoseq%2F1.50.0%2Bgalaxy0&version=latest).
The to…
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### Description of feature
Add creation of annotation database that can be used with Clusterprofiler and other R tools for GSEA,ORA etc
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It seems that the new version of ClusterProfiler is 4.12.6 according to the GiHub page.
I ran this script :
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocMan…
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Sorry to bother, I want to install old version 4.2.2. due to my previous analysis are done by this version. But I can't find a way to do this. Please can you tell me where can find the old release?
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eggNOG can functionally annotate a large number of non-model organisms. Once we are able to parse the output of eggNOG, we can easily combine it for analysis with GOSemSim and clusterProfiler.
see …
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### Is there an existing module for this?
- [X] I have searched for the existing module
### Is there an open PR for this?
- [X] I have searched for existing PRs
### Is there an open issue for this…
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I was confused by GO terms popped out in my GO analysis using enrichGO. For example, "GO:0141091: transforming growth factor beta receptor superfamily signaling pathway" was reported as one of the top…
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## Issue: qvalueCutoff parameter in enrichGO seems not working as expected
### Code Example
```r
go_mf args(enrichGO)
function (gene, OrgDb, keyType = "ENTREZID", ont = "MF", pvalueCutoff = 0.0…
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When using version 4.10.0 of clusterProfiler, the output from the enrichKEGG function shows that the Description column and ID information are identical, which did not happen with version 4.6.0. Is …
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Flo, en repassant sur les xml, j'ai noté sur les outputs :
1. ne devrait-il pas y avo…