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Irrationone / cellassign

Automated, probabilistic assignment of cell types in scRNA-seq data
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Bioconductor submission? #36

Open robertamezquita opened 5 years ago

robertamezquita commented 5 years ago

I saw some tags relating to bioc-check, and just wanted to check in on the status of Cellassign being submitted to BIoconductor. Thanks!

kieranrcampbell commented 5 years ago

Hi @robertamezquita

It's on the to-do list, and should be priority now. I'd been putting it off because of the tensorflow integration, which I'm not sure will play well with bioc, but will try and submit in the next week or so. Please let us know if any suggestions or requests.

Thanks

Kieran

LTLA commented 4 years ago

I've noticed that many of the issues in this repository relate around the installation of the Python dependencies. We've been working on resolving this in the context of Bioconductor packages by providing a central Python instance with a few core packages (including, yes, tensorflow). Repository here - check out the vignette and comments at LTLA/basilisk#2.

kieranrcampbell commented 4 years ago

Thanks Aaron, this could be a lifesaver. The python/tensorflow experience has not been great. I'll have a look into this when back from holiday in a couple of weeks.

kieranrcampbell commented 4 years ago

Hey @LTLA

Just made a version of cellassign that uses basilisk, seems to work nicely from my limited testing. What's the overall plan for the package? Is it going into the next Bioconductor release?

Thanks

LTLA commented 4 years ago

Is it going into the next Bioconductor release?

I hope so, but we're at a bit of a chicken-and-egg moment; I need to convince the core team that it's useful to get some support for it, but I can't do that until developers use it, and developers can't use it unless it's in Bioconductor.

So a good start would be to keep it on a separate branch but see if it solves any of the installation problems encountered by various users (only on Linux and Mac right now, though); this would provide the evidence of utility that I need.