[BioC] simple functional analysis of gene lists

[Rainer Tischler]

Dear all,

I have a script that generates a large number of gene sets (vectors of gene names) and would like to apply a functional analysis (e.g. how many transcription factors occur in each gene set? how many kinases... etc.). I can convert the gene names into different formats using biomaRt, however, the only functional analysis tools I have found in R apply an enrichment analysis on either GO or KEGG gene sets. Is there a package that allows me to answer more simple questions, e.g. just counting the number of transcription factors in a gene set by connecting to a public database?

Many thanks,
Rainer

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