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Single-Cell-Genomics-Group-CNAG-CRG / TICA_app

Tumor Immune Cell Atlas Shiny App
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Trouble with deconvolution on Shiny App #3

Open rgalvin516 opened 2 years ago

rgalvin516 commented 2 years ago

Hello,

I very much enjoyed your paper and thank you for your efforts at making an application for deconvolution of bulk RNA-seq available. I have great interest in giving it a shot with my dataset. The issue I am having is that once I upload my CSV file and the "Run" button appears, nothing happens and the app crashes. Thinking it is an issue with the file size, I have tried reducing my CSV file down to a single sample but the same thing happens. I was wondering if you had any thoughts or if it is possible to perform the deconvolution in my own R environment?

MarcElosua commented 2 years ago

hi @rgalvin516,

We will look into why it is crashing. In the meantime you can carry out the deconvolution using SPOTlight in R locally, you can find the vignette here.

Please let us know if you have any further questions!