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czbiohub-sf / tabula-muris

Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
https://www.nature.com/articles/s41586-018-0590-4
BSD 3-Clause "New" or "Revised" License
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Shiny App code #224

Closed jungminchoilab closed 3 years ago

jungminchoilab commented 4 years ago

Dear tabula-muris team,

This is a great resource. Thanks so much for sharing. I was wondering if you could share your shiny app code so I could visualize my scRNA-Seq data (Seurat v3.0 object) interactively.

Best, Jungmin

aopisco commented 4 years ago

@jungminchoi have you try using cellxgene https://github.com/chanzuckerberg/cellxgene ?

jungminchoilab commented 4 years ago

@aopisco Thanks for your prompt response. This is looking great but it does not look like it is compatible with Seurat yet if I understood correctly. Is this what was used in tabula-muris (https://tabula-muris.ds.czbiohub.org/) website?

aopisco commented 4 years ago

@jungminchoi that's a question for @neevor. As for using cellxgene with Seurat objects check this out: https://bioconda.github.io/recipes/r-sceasy/README.html

jungminchoilab commented 4 years ago

@aopisco Thanks!

neevor commented 4 years ago

@jungminchoi if you can use cellxgene that is the way to go. For the tabula muris site it's just a static website with pre-generated images, but the code used for any of the plots is in the notebooks in the repo. cellxgene is much easier and more flexible for a web interface though.