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EDePasquale / DoubletDecon

A tool for removing doublets from single-cell RNA-seq data
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Exporting Seurat object to the DoubletDecon app #36

Open Hatfield123 opened 4 years ago

Hatfield123 commented 4 years ago

Hello,

I'm very new to programming so I apologise if this is an annoying question.

I've used the Improved_Seurat_Pre_Process and would now like to use the DoubletDecon app to first test for rho-prime values and then run DoubletDecon, however I'm struggling to figure out how to export the Seurat object so that I can upload it to the app. Would someone be able to tell me how to do this?

Many thanks.

EDePasquale commented 4 years ago

Hi,

To simplify things, we have included the Improved_Seurat_Pre_Process() function in the app so you don't have to run it separately beforehand unless you want to use the command line version of DoubletDecon. All the UI needs is the Seurat object (prior to Improved_Seurat_Pre_Process()), which can be saved by following the code in the "seurat-3.0.R" file located in this repository. If you haven't before, please check out our protocol and the vignette located in the Wiki.

Let me know if you have any more questions! Best, Erica