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GO Enrichment with poorly annotated genome

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

gsea go oryculus scrna
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written by HERMAN • HERMAN

1 answer

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.

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written by Jean-Karim Heriche Jean-Karim Heriche

Thank you very much !

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written by HERMAN • HERMAN

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