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aertslab / SCopeLoomR

R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...
MIT License
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How to convert the loom file to seurat object? #9

Closed Sophia409 closed 4 years ago

Sophia409 commented 5 years ago

I need to merge my seurat data with the data provided by loom edition(http://mousebrain.org/tissues.html).But I don't know how to convert this loom file to seurat object, so that I can merge them with my own data and do next analysis. I didn't see this function in your tutorial. I tried to get the matrix and meta data from loom file,and use them to crea tseurat object,but I don't see how to get metadata from loom in your tutorial either. So what should I do to convert the loom file to seurat object? Can you give me some help?Thank you very much! Sophia @tropfenameimer @ghuls @KrisDavie @cflerin @sedjro

dweemx commented 5 years ago

Hi @Sophia409, Currently, there is no implemented function in SCopeLoomR to convert a loom to Seurat however you should be able to do this with loomR (see https://satijalab.org/loomR/loomR_tutorial.html, section Creating a loom object from a Seurat object (converting between Seurat and loom))

Sophia409 commented 5 years ago

Thank you!But the tutorial says that : Seurat offers a conversion function to go from Seurat objects to loom files. The reverse conversion is currently in progress. Does it means that I could't convert loom file to seurat?So what should I do to convert the loom file to my seurat object? Or how to merge loom file with my seurat object?Can you give me some help?Thank you very much! default @mase5

dweemx commented 4 years ago

You could try sceasy + Seurat::ReadH5AD

dweemx commented 4 years ago

Considering this as a closed issue