4
votes
GOseq analysis with evidence code filter
A bit weird to answer my own question, but for who's interested I can show the 'hard' way using biomaRt and then use goseq with <...
- 3,591
3
votes
Accepted
How to run enrichment analysis of protein functional annotation?
DAVID depend on a couple of databases from the Gene Ontology Consortium, Reactome, KEGG,... most of them are accessible via Bioconductor. To perform an enrichment analysis you can have a look at the ...
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3
votes
How to run enrichment analysis of protein functional annotation?
I would recommend R instead of sticking to websites.
There are many tools for enrichment analysis. I like to use GOseq, which is initially made for RNAseq data, but can also be used for proteins (I ...
- 3,591
2
votes
Correct for gene length or read counts in GO enrichment analysis
My understanding of the subject is that the bias of the gene length (and other bias) should be taken care when analyzing the expression and before enrichment analysis. The enrichment analysis should ...
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2
votes
Number of edges in Graphical Analysis using Jupyter with Go Programming language
the dot file in the Git repo has 6646 edges, the pajek file in your link has 7182.
Chances are the latter has been updated since.
2
votes
Accepted
Choosing Fisher's Exact or Binomial test for overrepresentation in PANTHER
For a guide on using the tests in PANTHER, see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6519457/.
In answer to this specific question, the defaults are the best choice (Fisher's Exact Test, with ...
1
vote
Accepted
eggNOG: DNA-DNA or protein-protein orthologue identification?
I can answer this now. I've been 'under the hood' of eggNOG and its using "hmm" (hidden Markov model) very likely, almost certain, the Eddie (sp?) group's ...
M__♦
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1
vote
After KEGG and GO analysis, how to make tables+phylogenetic trees
I'm going to answer 1+2 because 3 is hard to understand and maybe trivial?
Each of 1+2 seems to be have these sub-tasks:
identify the contigs in your assembly that have the genes of interest.
pull ...
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1
vote
Correct for gene length or read counts in GO enrichment analysis
I am not sure if it makes sense to use read counts as bias instead of gene length (and I certainly wouldn't expect the same results).
Do you use total read counts of all your samples (library size)? ...
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