Seurat compatibility feature requests

[akramdi]

Hi,

This is not a question but rather a need for clarification. I am confronted with some limitations due the input data being Seurat objects. For instance, detection of gene markers is currently not supported (addressed in #16)

Could it be possible clarify which downstream analyses is possible in this case ? I imagine that this might change with future enhancements, but it'll be very useful to mention it clearly in the vignette.

Thank you !
Best,

[evanbiederstedt]

Hi @akramdi

Thanks for using conos!

It's a good question of course. The issue here is really keeping up with Seurat changes, and fully integrated them into the code---I think the lab doesn't have the bandwidth to do this, as it's a major investment. We certainly welcome pull requests and contributions from the community though!

For instance, detection of gene markers is currently not supported (addressed in #16)

With regards to this, you may want to consider using the pagoda2 frontend application with a conos object. We discuss this a bit in the vignettes (now in the dev branch, but we hope to push to the main branch soon): https://github.com/kharchenkolab/conos/blob/dev/vignettes/walkthrough.Rmd#L635-L645

"""
After constructing the con object as shown above, users can save to a serialized *.bin file and upload into the pagoda application with the p2app4conos() function, using p2app4conos(conos=con). More information, please review the Pagoda2 walkthrough

library(pagoda2)
p2app = p2app4conos(conos=con, file="conosApp1.bin", save=TRUE)
show.app(app=p2app, name='conos_app')

"""

It won't give you precisely what you are looking for I suspect, but you will be able to detect the marker genes.

Could it be possible clarify which downstream analyses is possible in this case ? I imagine that this might change with future enhancements, but it'll be very useful to mention it clearly in the vignette.

But to answer your question, I think you need to tell us :) I'm happy to edit the vignettes for users. If there are certain features you'd like, we could try to implement them (if time allows, etc.)

I hope that's helpful. Best, Evan

[akramdi]

Hi Evan,

I understand. I'll take a look at pagoda2. Thanks for the links and code !
I'll carry on then and will let you know if I'm confronted with errors that could be related to Seurat objects (maybe other users will in this issue).

Best,
Amira

[evanbiederstedt]

Hi Amira

Sounds reasonable. I'll leave the issue open with a "help wanted" label.

As I say, we're happy to include pull requests and contributions from the community!