Merged+clustered data saved in format suitable for uploading to Broad's single cell portal / CellXGene

Question

Merged+clustered data saved in format suitable for uploading to Broad's single cell portal / CellXGene

NathanSkene opened this issue 5 years ago · 3 comments

Answer 1 · 2019-12-11T13:32:23.000Z

The BSCP wiki describes the format clearly and it seems a sce_to_bscp() function to generate the bscp objects from a SingleCellExperiment, and a write_bscp() function to write them should be straightforward to implement.

That said the current functionality of the BSCP seems sparse to me; would be open to implementing our own explorer unless they have more features in the pipeline / it's under active development.

Answer 2 · 2019-12-11T15:55:26.000Z

I'll be going there to have a chat with them in Jan. Will suggest to them a list of things which should be improved: including being able to push datasets to it directly. If you've got any ideas for features that it should have then list them here! How would you go about creating your own explorer? Using Shiny? Maybe you are right that we should do that. On 11/12/2019 13:32, Combiz Khozoie wrote: This email from notifications@github.com<mailto:notifications@github.com> originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. The BSCP wiki describes the format clearly and it seems a sce_to_bscp() function to generate the files from a SingleCellExperiment should be straightforward to implement. That said the current functionality of the BSCP seems sparse to me; would be open to implementing our own explorer unless they have more features in the pipeline / it's under active development. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#30>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AH5ZPEZRDWUKERUDEMA3BSDQYDTWPANCNFSM4JY3VSIA>.

Answer 3 · 2019-12-11T16:29:32.000Z

Sure, can put together a feature list. Meeting them should also help figure out how actively it's being developed!

If we were going it alone, I think Shiny would be a strong first choice followed by Dash / Python. Another interesting approach would be a newcomer called ~~Svelte~~ Streamlit which has been receiving a lot of attention lately.