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2 votes
1 answer
54 views

Calculating Fisher's exact test for COG categories

This is a continuation of the following question - Fisher's exact test for COG categories in pan, core genome analysis Also, the dataset - How do I perform a Fisher's exact test on this data to ...
1 vote
1 answer
99 views

Fisher's exact test for COG categories in pan, core genome analysis

I have come across several papers that do a Fisher's exact test to show over represented genes in COG categories specifically in a pan-core-accessory-species specific genome analysis. The test is done ...
2 votes
2 answers
67 views

Error with eggNOG-mapper jobs

I recently tried using eggNOG-mapper for pan-genome and core genome analysis of files from OrthoFinder, specifically the 'Orthogroup_Sequences' which contains a huge list of protein files in fasta ...
2 votes
0 answers
110 views

COG Enrichment, the overrepresentation test between annotated transcriptome and a set of annotated gene, eggnog-mapper annotation results

I am dealing with a transcriptome of a species and list of genes selected for a gene enrichment analysis. In order to see what kind of genes in my selected list are overrepresented compared with the ...
1 vote
0 answers
60 views

eggNOG API, how's it work?

Background eggNOG uses seed orthologues which correspond to its own internal database, so for example J421_1876 can be placed in its online search engine here. This ...
1 vote
1 answer
62 views

eggNOG: DNA-DNA or protein-protein orthologue identification?

I'm trying to work out is how reliable/accurate my eggNOG metagenomic outputs are. Critical for this is how its identifying orthologues. Background eggNOG is ...