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This means adding the cell counts for each cell type to each SPE object (the versions that will be uploaded to shiny + #76). This could be done directly on the `app.R` scripts (if so, update the `depl…
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- [x] snRNAseq MDD https://pubmed.ncbi.nlm.nih.gov/32341540/
- [x] snRNAseq ASD https://pubmed.ncbi.nlm.nih.gov/31097668/
- [ ] DOUBLE CHECK: bulk sex differences SCZ https://www.biologicalpsychiatr…
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In the clustering results saved at `/dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/processed-data/rdata/spe/clustering_results`, e.g.
`/dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/sp…
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This will be done only with the n = 4 Visium IF samples. It will depend on results from several other issues https://github.com/LieberInstitute/spatialDLPFC/issues?q=is%3Aissue+is%3Aopen+label%3Aspot-…
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Related to from spatial-DLPFC [Issue #82](https://github.com/LieberInstitute/spatialDLPFC/issues/82#issue-1228672846) and [Issue #76](https://github.com/LieberInstitute/spatialDLPFC/issues/76#issue-12…
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Take the default files in `spatialLIBD` and start editing them. Save them at https://github.com/LieberInstitute/spatialDLPFC/tree/main/code/deploy_app and update the `deploy.R` and `app.R` scripts. Se…
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Some spot plots created by `spatialLIBD::vis_gene()` of samples are forced out of the correct aspect ratio when saved to pdfs. This is because the image is often not a square. However the fiducial fra…
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`/dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/psychENCODE/version2`
- [ ] problem with DupCor() getting stuck. probably because of covariates.
- [ ] remove covariates all…
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This would be similar to https://bioconductor.org/packages/release/data/experiment/html/scRNAseq.html or `spatialLIBD::fetch_data()` or http://bioconductor.org/packages/release/data/experiment/html/ST…
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Similar to https://github.com/LieberInstitute/spatialDLPFC/issues/80. Maybe Heena could help with this one? We'll figure it out.