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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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Data integration #14

Open sespesogil opened 2 years ago

sespesogil commented 2 years ago

Hi! Congrats for the study! Very nice!

I am integrating more data into your TICA atlas and I am following the approach you use here: https://github.com/Single-Cell-Genomics-Group-CNAG-CRG/Tumor-Immune-Cell-Atlas/tree/main/Integration It is kind of working up the last step and I am wondering if your script that you source several times during the process: source("code/functions/load_objects.R") is doing something else than just creating a list of Seurat objects and loading them. Would it be possible if you could share that script? That will help me to figure out what is going on.

Thanks in advance! Really appreciate it.

S.

sespesogil commented 2 years ago

I have solved it. No need to share the script.

Also wondering, if you could answer a small question regarding the naming you followed in the Seurat metadata, as it is not exactly following the same labels as in the supplementary material. Could you confirm that M2 TAMs are the same as in shown in Supplementary Table 4 as TAMs C1QC? It is maybe obvious , but if you could confirm that would be great. Thanks!

PaulaNietoG commented 2 years ago

Hi! Yes, possibly you are using an older version of the object. In the final object, although we have two levels of annotation, there sould only be the TAMs C1QC cells.

sespesogil commented 2 years ago

Ok, I see where this is coming from. Would be ok if you could change in the Github repo the actual final data repo you used in the paper? See that it is pointing to the pre-print version. Thanks!