Shiny app for already analyzed Seurat objects

[elimereu]

Dears developers,

thanks a lot for providing this nice shiny app. It is something really useful. However, I recently discovered that and I have my scATAC-seq data already analyzed as a R object. I wonder if your app enable to directly upload a Seurat object.

[ankushs0128]

Hi Elimereu , Unfortunately , At the moment, ShinyArchR.UiO doesnot support Visualization from scATAC-seq Seurat object.

[elimereu]

Ok, thanks for the prompt response!

That’s a pity bc you are using Seurat inside, isn't?

Il giorno 11 mag 2023, alle ore 15:46, Ankush Sharma @.***> ha scritto:

Hi Elimereu , Unfortunately , At the moment, ShinyArchR.UiO doesnot support Visualization from scATAC-seq Seurat object.

— Reply to this email directly, view it on GitHub https://github.com/EskelandLab/ShinyArchRUiO/issues/5#issuecomment-1544028097, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE5OXS5YRL63TWRV3ARQCX3XFTUVDANCNFSM6AAAAAAX5ZQM4A. You are receiving this because you authored the thread.

[ankushs0128]

We are planning to include other objects in upcoming releases . Closing issue for now. Thanks

[ankushs0128]

hi @elimereu, Ideally what plots would you like to visualize in ShinyArchR from Seuratobject? We may be able to put it up something supporting UMAPS and Coverage plots in the next few days. If that works for you?

[elimereu]

Hi Ankush,

Thanks for following up with it. Yes, it would be great to explore UMAPs with the different metadata and coverage plots.

Keep me posted,

Elisabetta

Il giorno 13 mag 2023, alle ore 13:33, Ankush Sharma @.***> ha scritto:

hi @elimereu https://github.com/elimereu, Ideally what plots would you like to visualize in ShinyArchR from Seuratobject? We may be able to put it up something supporting UMAPS and Coverage plots in the next few days. If that works for you?

— Reply to this email directly, view it on GitHub https://github.com/EskelandLab/ShinyArchRUiO/issues/5#issuecomment-1546627940, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE5OXS45IQQOCRSTCFMZQMLXF5WO5ANCNFSM6AAAAAAX5ZQM4A. You are receiving this because you were mentioned.

[ankushs0128]

Hi Elisabetta , @elimereu Please feel free to test the visualization on Seurat Objects https://github.com/EskelandLab/ShinyMultiomeUiO.

best Ankush

[ankushs0128]

Closing for now here , please open an issue on https://github.com/EskelandLab/ShinyMultiomeUiO

[elimereu]

Dear Ankush,

Thanks a lot!!! I will test you ASAP and let you know in case of any issue.

Best wishes,

Elisabetta

Il giorno 21 giu 2023, alle ore 09:20, Ankush Sharma @.***> ha scritto:

Hi Elisabetta , Please feel free to test the visualization on Seurat Objects https://github.com/EskelandLab/ShinyMultiomeUiO https://github.com/EskelandLab/ShinyMultiomeUiO.

Ankush

— Reply to this email directly, view it on GitHub https://github.com/EskelandLab/ShinyArchRUiO/issues/5#issuecomment-1600311672, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE5OXSYJEYEQABE7YC5QNI3XMKOFFANCNFSM6AAAAAAX5ZQM4A. You are receiving this because you were mentioned.