goatools
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tanghaibao
Python library to handle Gene Ontology (GO) terms
When I ran an enrichment study, I was getting the warning: "1 GO IDs NOT FOUND IN ASSOCIATION" I looked into the code, the warning is printed at line 43...
Is it possible for the GOEnrichmentRecord objects to provide the change from expected representation in a group?
Greetings! My study team has been looking at using GOATools for comparison of two groups of prokaryotic genomic entities in metagenomics assemblies. Here we are looking for the presence of...
I'm getting a real low FDR/pVal for GO:0004930, where there is only 1 gene that matches. I'm nervous that either something is wrong or I'm passing in the wrong thing....
Hi all. I am running goatools v 0.6.10. The result for an enrichment analysis shows a very large pvalue-qvalue difference which sounds strange to me. Here is the command line:...
I am running find_enrichment.py of a Denovo transcriptome assembly, and I want to have it as a description of the GO abundance in my nonmodel plant transcriptome. Given that my...
Hi, I have been trying to use find_enrichment.py to perform an enrichment analysis. I originally tried it with my study but it did not work so I tried it with...
Dear @tanghaibao, I'm implementing a go-term enrichment analysis not directly based on genes but on cis-regulatory regions acting on nearby genes. At the moment I can test all go terms,...
I do the following analysis: I have a complete list of genes from a modern genome. Also, I have a complete list of genes from an ancestor of this species...
Hello, Thanks for developing and maintaining this amazing resource. There is [an instruction](https://github.com/tanghaibao/goatools/blob/main/notebooks/dcnt_and_tinfo.ipynb) to obtain information content for each GO term in human, mouse, and fly GOA. Could you also...
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Python library to handle Gene Ontology (GO) terms