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romanhaa / Cerebro

Visualization of scRNA-seq data.
MIT License
93 stars 19 forks source link

Loading in multiple seurat object #25

Closed f0ng1203 closed 4 years ago

f0ng1203 commented 4 years ago

Hi,

Thanks for the great app. I find it very useful to use your app. However, currently I am facing some issues with loading in files.

Based on your example, you load in 4 different H5 files which were produced by 10X Cell Ranger.

For me, I have a hashtag data. I proceeded to demultiplex it and currently I have one big seurat object with all the identifiers. I proceeded to break it down into 5 individual seurat objects (I have 5 groups) and I am lost here. I don't know how to load it into CerebroApp.

Could you offer some advice?

Thank you very much.

regards, Fong

romanhaa commented 4 years ago

Hi Fong,

I apologize for the long wait before replying. What you'll have to do is export the Seurat objects into a format that is compatible with Cerebro. You can find an example workflow here: https://romanhaa.github.io/cerebroApp/articles/cerebroApp_workflow.html

I hope that helps!

Best, Roman

f0ng1203 commented 4 years ago

Roman,

Thanks. I have managed to make it work.

Regards, Fong

romanhaa commented 4 years ago

Great!