adata processing issue?

[daniel-spies]

Hi there and thanks for the great tool. I'm trying to get started by supplying an annData object to cogaps in python. When I print all parameters though with params.printAllParams() it displays the tranposed information of nGenes and nSamples. Also in your tutorial the data results matrix has it inverted compared to the annData / scanpy annotation, is this only for the results matrix or also internally (as R is handling it the other way round I think)

So I'm wondering if this is just an annotation mistake or if your tools in the background correctly reads in the annData object. For now I'll try to run it with the transposeData: TRUE option.

or should I rather use the distributed: 'single-cell' instead of the 'genome-wide' option?

best
Daniel