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LieberInstitute / spatialDLPFC

spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
http://research.libd.org/spatialDLPFC/
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snRNA-seq issues #88

Closed lcolladotor closed 2 years ago

lcolladotor commented 2 years ago

Either re-locate or update the issues from https://github.com/LieberInstitute/DLPFC_snRNAseq/issues to here. Update the issues based on our meeting on Friday.

Thanks Louise!

lcolladotor commented 2 years ago

It'll involve also adapting issues from https://github.com/LieberInstitute/Habenula_Bulk/issues?q=.

Once these are updated here, then @joshstolz will need to update the ones for Habenula, as we want to process these two datasets in a similar way.

lcolladotor commented 2 years ago

Note that we discussed how we are planning to use reducedMNN() in the snRNA-seq data but have used harmony in the spatial data https://doi.org/10.1038/s41592-019-0619-0. For now we decided to use reducedMNN() and GLM-PCA-approx in the snRNA-seq data. Exploring how it looks with harmony is optional but could be done on the side or in another smaller project like Habenula.

lahuuki commented 2 years ago

@lcolladotor and I decided to keep DLPFC_snRNAseq as its own Repo