how to calculate GO enrichment analysis for all predicted complexes ?

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Torsten Semmler

I recommend OmicsBox with its Functional Analysis modul, the former Blast2GO.

https://www.biobam.com/omicsbox/ There is a trial version available.

Didem Okmen

You can use:.

GOstats

http://www.bioconductor.org/packages/release/bioc/vignettes/GOstats/inst/doc/GOvis.pdf

topGo https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf

Rajesh Durairaj

Hi, I suggest

1.STRAP for GO Annotation (http://www.bumc.bu.edu/cardiovascularproteomics/cpctools/strap/),

2.BLAST2GO;

3. REVIGO by Panther enrichment values to make a protein complex network map.

Hope its useful.

Rajesh