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cellgeni / sceasy

A package to help convert different single-cell data formats to each other
GNU General Public License v3.0
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Plans to submit to BioC? #5

Open LTLA opened 4 years ago

LTLA commented 4 years ago

I would be very interested in seeing this package submitted to Bioconductor. Are there any plans for this? For starters, I would be very pleased to be able to excise the monocle conversion code out of scran if I had a central "conversion hub" package that I could move that code to.

Depending on basilisk's progress, you may even be able to alleviate your SystemRequirements.

nh3 commented 4 years ago

Very good idea @LTLA ! We are working on it.

LTLA commented 4 years ago

Excellent. When you get closer to submission, I would be happy to make a PR to move the SCE <-> monocle2 conversion code from scran into your package. (It may also be worth reaching out to @hpliner to see what data structure monocle3 ultimately decided to use.)

LTLA commented 4 years ago

Come to think of it, I'll even throw in the SCE <-> edgeR's DGEList and DESeq2's DESeqDataSet if you want - basically everything in scran::convertTo, all for the low, low price of nothing.