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waldronlab / TENxIO

Bioconductor interface to 10X files
https://bioconductor.org/packages/TENxIO
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import read10xVisium function #3

Open drighelli opened 1 year ago

drighelli commented 1 year ago

As already discussed multiple times with @LiNk-NY and in some other issues around, it would be nice to have all the import functions into a unique package. We think this would be a nice container for all of them.

So, Marcel asked me to import the read10xVisium function into this package to remove dependencies like dropletUtils from our SpatialExperiment class so I'm linking @lmweber and @HelenaLC to see if they agree with this process

lmweber commented 1 year ago

Yes, I think this makes sense to me, so there would be more of a separation between the core class (SpatialExperiment) and specific helper / loading functions that are only relevant for for certain platforms (read10xVisium()).

This would then also solve the DropletUtils dependencies issue in #139.

Is the plan also to import read10xCounts() from DropletUtils into the TENxIO package? Either way it would be good to have consistency between how read10xCounts() and read10xVisium() are handled.