Closed lcolladotor closed 2 years ago
@Nick-Eagles will help download https://doi.org/10.7303/syn30108587.1 to raw-data/psychENCODE
or something like that
maybe add a version1
sub-directory since we anticipate that they'll have multiple versions
Hmmm, while the project itself is supposedly open access, individual files like the first one are restricted access. Am I missing something?
Nick and I confirmed this and I emailed Juliane in order to give Nick access to these files.
We resolved the access issues, and the files are now downloaded at /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/psychENCODE/version1/
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.
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.
This data is now downloaded under raw-data/psychENCODE/version2
Awesome, thanks @Nick-Eagles! Can you check it @abspangler13? Thanks.
I think was done mostly by Abby already.
spatialLIBD
function for computing "enrichment" t-statistics, which will make the next step easier