Lukas Heumos

Can they also be made interactive? I don't know which R libraries you are using, since I am only familiar with Python based stuff, but would be useful if the...

Oh, I thought this issue was referring to the HTML report, which could contain interactive elements.

scrublet doesn't seem to be part of the benchmarks at the moment

That's because the newer EFO version is broken. See: https://github.com/EBISPOT/efo/issues/2264 (also for a solution). I can read EFO 3.70+ by fixing the owl file as outlined in the thread. Nevertheless,...

@emdann @xinyuejohn started with the integration of milopy into pertpy here: https://github.com/theislab/pertpy/pull/165 He could also tackle my feedback that I posted here if it's fine with you? Then we don't...

> Therefore, if I need to add a `mdata = milo.load()` function, it should substitute the original `milo.count_nhoods` function. What do you think? Do you think it follows the best...

Theislab dude here. Just wanted to say that we have some people working on batchGLM again and I think that it would be a good choice for you in the...

> Hi @Zethson, thanks for the heads up. I actually have some bandwidth now to look into this and try a few options out. Well, batchglm will still take a...

Excellent @picciama ! Thank you very much! Really think that a Python native edgeR will be super useful for the community. Just a big bonus that we can add this...

BTW @picciama this is where the new batchGLM based implementation should then end up in -> https://github.com/theislab/pertpy/blob/development/pertpy/tools/_milopy.py#L306 (Just another if case)