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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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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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### 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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## 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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R version
4.3.1
packageVersion("clusterProfiler")
‘4.10.1’
get_wp_organisms() gives:
"Caenorhabditis elegans" "Bos taurus" "Arabidopsis thaliana"
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writen code:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("clusterProfiler")
console output:
> if (!require("BiocManager", quietly = TRU…
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### Prerequisites
+ [x] Have you read [Feedback](https://guangchuangyu.github.io/clusterprofiler/#feedback) and followed the [guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/)?
*…
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I am performing a GO enrichment analysis using genes from the transcriptome as the reference universe, consisting of 23,761 genes. I then conducted an enrichGO analysis on my differentially expressed …
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Flo, en repassant sur les xml, j'ai noté sur les outputs :
1. ne devrait-il pas y avo…
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I have used [GSVA](https://github.com/rcastelo/GSVA) and [GenePattern](https://github.com/GSEA-MSigDB/ssGSEA-gpmodule) or [GenePattern ](https://github.com/broadinstitute/ssGSEA2.0) for ssGSEA, GSVA d…