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Single-Cell-Genomics-Group-CNAG-CRG / Tumor-Immune-Cell-Atlas

Code repository for the Tumor Immune Cell Atlas (TICA) project
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Genes #12

Closed afitz-gmu closed 2 years ago

afitz-gmu commented 2 years ago

Hi, I am looking through the new matrix of genes x expression uploaded to zenodo. I am noticing that I can't find some genes in that file that are located in your shinyapp. When I pull out all the first column gene names it only totals 4419 genes. I am wondering if only some of the data was uploaded or if this is a known problem.

Thanks!

PaulaNietoG commented 2 years ago

Hello! This is because the matrix only contains the integrated data. If you download the .rds or .h5ad files you will have the complete objects there. Thanks a lot for your interest in our work!

afitz-gmu commented 2 years ago

Hi, thanks so much for getting back to me. If I am looking for just one specific gene is there an easy way to manipulate these files for that gene? The files are so large that I'm having some issues. Thanks!

PaulaNietoG commented 2 years ago

Hello, unfortunately, no, there is no easy way... However, if you just want to check the expression of that gene, you can visualize it using our Shiny App, otherwise if you need to extract raw/normalized counts for that gene(s), you will have to manipulate the whole object.