GO Enrichment with poorly annotated genome

Question

[HERMAN]

Hi Biostars,

I'm currently working with 10X single cell data and have come to clustering. Although my topmarkers define pretty well who's who, i'd like to give a try with Gene ontology analysis.

I'm a noob regarding those methods and I'm struggling with what to do. I've got a list of clusters ( 10 ) and for every cluster I've calculated the mean expression of each gene within the cluster. I'd like to run some sort of GSEA analysis but I have not found any easy to use R package.

Because I'm working with a Rabbit genome ( Oryculus cuniculus ), databases are fairly poor. Thereby i've downloaded from Biomart the complete list of genes + GO number + Ensembl ID + verbal description of biological function.

Are there packages that do not rely on Human GO or on web services like DAVID or Panther ? Is it possible to manually analyse my gene-GO file with my expression data ?

Best regards, Simon

Answer 1

[Jean-Karim Heriche]

There are a number of R packages that support many non-human organisms and/or that allow to use custom annotations. Check for example clusterProfiler and topGO.

[HERMAN]

Thank you very much !