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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 <...
benn's user avatar
  • 3,581
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 ...
llrs's user avatar
  • 4,713
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 ...
benn's user avatar
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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 ...
llrs's user avatar
  • 4,713
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.
Bastian Schiffthaler's user avatar
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 ...
Paul D. Thomas's user avatar
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__'s user avatar
  • 12.6k
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 ...
Maximilian Press's user avatar
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)? ...
benn's user avatar
  • 3,581

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