The result files of Stereoscope are missing

Swarbricklab-code / BrCa_cell_atlas

Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".

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The result files of Stereoscope are missing #9

Closed yewero closed 2 years ago

yewero commented 2 years ago

Specifically, there are 3 related files: https://github.com/Swarbricklab-code/BrCa_cell_atlas/blob/adfbc29d4dc628336c2c2593cdc638b8c0a7d370/spatial_analysis/append_stereoscope_data.R#L40-L50 How could I find these files?

johnyaku commented 2 years ago

I've added the Stereoscope results to spatial_analysis/stsc. I've fixed some of the paths in append_stereoscope_data.R but some are still specific to our HPC cluster. You might have to adjust some more paths to get the script to run (and please open a pull request if you do!) but at least you can explore the data. Sorry about the hold up.