Scanpy: Auto-generation of Study files for Single Cell Portal submission

[sjfleming]

I have recently been using scanpy to analyze my data and get it into a format that I want to share with others. I've been doing that using the Broad's Single Cell Portal, which I suspect others use as well. It took me a couple of hours to figure out the details of file formatting, etc, but I realize the process could be easily automated. Given an adata object, a list of files can be generated that are formatted correctly for upload. I have written this function and I use it myself.

Is scanpy interested in a function that does this? Where in the code would such a thing go?

I'd be happy to create a pull request, but didn't want to go ahead unless there's interest.

Or maybe anndata is a better place for something like this?

[ivirshup]

I think this could be useful, but I'm not sure how stable their format is, or if we can promise to support it. Maybe this could be a standalone package which we link to from the docs?

Thoughts @flying-sheep?

[fidelram]

This sounds great. If I recall correctly it is possible to upload data to
the broad single cell portal and share this link with other people right?
This would certainly be useful.

On Tue, Dec 10, 2019 at 4:23 AM Isaac Virshup [e-mail]
wrote:

I think this could be useful, but I'm not sure how stable their format is,
or if we can promise to support it. Maybe this could be a standalone
package which we link to from the docs?

Thoughts @flying-sheep https://github.com/flying-sheep?

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
https://github.com/theislab/scanpy/issues/950?email_source=notifications&email_token=ABF37VJIYCEDQNKTLEB3V23QX4DS7A5CNFSM4JXFVOAKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGMRPJY#issuecomment-563681191,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/ABF37VKHFTRDL6MDRBWAJ33QX4DS7ANCNFSM4JXFVOAA
.

--

Fidel Ramirez

[gokceneraslan]

(Orthogonal to this suggestion: We can maybe talk to the SCP people and ask how difficult would it be to use h5ad as a native format.)