Process psychENCODE datasets

[lcolladotor]

• [x] Wait till they actually give us access to this data
• [x] Download their processed data
• [ ] Revisit older code from https://github.com/LieberInstitute/HumanPilot/blob/master/Analysis/Layer_Guesses/ad_snRNAseq_recast.R https://github.com/LieberInstitute/HumanPilot/blob/master/Analysis/Layer_Guesses/allen_brain_layer_compare.R https://github.com/LieberInstitute/HumanPilot/blob/master/Analysis/Layer_Guesses/asd_snRNAseq_recast.R to see how we dealt with different study designs.
• [ ] allen brain analysis https://github.com/LieberInstitute/HumanPilot/tree/master/Analysis/allen_data
• [ ] Explore the study designs: some might be complicated and we might need to think about the correlation structure. What cell types do they have? What diseases do they have?
• [ ] (optional) Make list of questions for psychENCODE authors to clarify their datasets and/or make suggestions to improve their documentation
• [ ] (optional) re-shape their processed data into SCE objects. This will depend on the file format they will use
• [x] (optional but encouraged) finish spatialLIBD function for computing "enrichment" t-statistics, which will make the next step easier
• [ ] Run spatial registration and make plots.
• [ ] If they provide lists of DEGs, split by direction, then also run clinical enrichment analyses
• [ ] Export results for #79

[lcolladotor]

@Nick-Eagles will help download https://doi.org/10.7303/syn30108587.1 to raw-data/psychENCODE or something like that

[lcolladotor]

maybe add a version1 sub-directory since we anticipate that they'll have multiple versions

[Nick-Eagles]

Hmmm, while the project itself is supposedly open access, individual files like the first one are restricted access. Am I missing something?

[lcolladotor]

Nick and I confirmed this and I emailed Juliane in order to give Nick access to these files.

[Nick-Eagles]

We resolved the access issues, and the files are now downloaded at /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/psychENCODE/version1/

[lcolladotor]

Awesome, thanks Nick! Abby @abspangler13 can you take a look at those files? You might need to meet with Nick in order to learn how to import that data into R. http://bioconductor.org/packages/release/bioc/html/zellkonverter.html might be useful.

[Nick-Eagles]

Update: Prashant (collaborator) is updating some of the .h5ad-based data, after which I'll download the updated dataset and work with Abby to make sure we can load things into R.

[Nick-Eagles]

This data is now downloaded under raw-data/psychENCODE/version2

[lcolladotor]

Awesome, thanks @Nick-Eagles! Can you check it @abspangler13? Thanks.

[lcolladotor]

I think was done mostly by Abby already.