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Once we have selected the deconvolution marker genes from #127, at _broad cell type_ and _layer level_ resolutions run:
- [x] Tangram (Related to #96)
- [x] cell2location (Related to #97)
- [x] S…
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Related to #80
This one will be challenging due to memory issues as it's a large dataset. We might have to do this one outside shinyapps.io and recruit Bill's help to setup an AWS machine to run t…
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Maybe move some of the older scripts from https://github.com/LieberInstitute/spatialDLPFC/tree/c61820105268869abff3cbfa029e97827b670073/code/analysis to `old` or something like that. That way the new …
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find in OSCA the part where they talk about running PCAs. Make plots they suggest to check this. Check with Matt too to see what he did for his data.
https://github.com/LieberInstitute/spatialDLPF…
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Heena will run `spaceranger` for the IF samples @shkwon17 is generating and that @madhavitippani is segmenting. This will involve new sequencing data and new images.
![IMG_7149](https://user-ima…
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This likely can be done with `mv` commands or directly from Cyberduck by Louise because both are already at `/dcs04/lieber/lcolladotor`. We'll need to check first that the ACLs are the same in both (`…
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Hi Abby,
Can you make the plots for the marker genes? That will involve updating https://github.com/LieberInstitute/spatialDLPFC/blob/32a14108b4ccc2210f1f8f63857d51f4847f6994/analysis/02_marker_gen…
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- [x] Run `cellpose` on all channels with the n = 4 Visium IF samples
- [x] Extract per-cell metrics on a CSV file: include either the `key` column (combines barcode ID with sample ID like at https:/…
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We will pseudo-bulk the Visium n = 30 samples in different ways. Given that `spatialLIBD` only has one pseudo-bulk level panel, and since we want users to be able to explore the data from the differen…
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This involves input from Maddy and others working with Matlab. Once we have the estimated number of cells per spot from Joe's code, we can then read in the data and add it to our `sce` object using ht…