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LTLA / scRNAseq

Clone of the Bioconductor repository for the scRNAseq package.
http://bioconductor.org/packages/devel/data/experiment/html/scRNAseq.html
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Adding Tabula Muris Senis datasets #34

Closed StefaniAstrologo closed 3 years ago

LTLA commented 3 years ago

A bit of context would help. For example, we already have a TabulaMurisData package - perhaps this data would find a more appropriate home there? Tagging @csoneson.

Also, no need to use such a convoluted sequence of packages to read a H5AD file into an SCE, that's what zellkonverter is for.

csoneson commented 3 years ago

Yes, we do have a TabulaMurisData package in Bioconductor - and as a matter of fact, we were just in the process of submitting a TabulaMurisSenisData one...the repository is here. @StefaniAstrologo - did you already upload the data? Perhaps in any case we can move this discussion to the TabulaMurisSenisData package repository and see how we can best move forward/combine things.

StefaniAstrologo commented 3 years ago

Hi @LTLA! I have to admit I wasn't aware of the TabulaMurisData package. Sure we can combine things @csoneson if there is anything left that is useful :) About zellkonverter: while using this package to open the h5ad files it returns an empty dgMatrix. I tried to change the code of the function without success and then I went for this inelegant solution.

LTLA commented 3 years ago

I'm going to close this, assuming that you two can combine your efforts in TabulaMurisSenis.

A MRE on how zellkonverter fails would also be helpful if it is posted to the relevant repo.