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ncborcherding / utility

Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
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v.04 data with sample annotation #5

Closed p-gueguen closed 1 year ago

p-gueguen commented 1 year ago

Hello,

Thanks a lot for the nice repo! I was wondering if you had a version of the v0.4 datasets with annotated Type, Tissue, and the Cohort (with the GSE identifier for instance) in the metadata, like what you had for the v0.1 pipeline.

I can retrieve most of it by your sample name nomenclature, but I think I will still miss the cohort identifier.

Thanks a lot for your help, Paul

ncborcherding commented 1 year ago

Hey Paul,

I am working on making a single integrated object which will include the cohort data. For now, each of the sequencing runs are summarized here. Hope that helps.

Nick

p-gueguen commented 1 year ago

Thank you for the quick answer, Nick! Looking forward to the updates on this. I had missed the excel file indeed. Is there any way to match these metadata to the samples of individual Seurat objects (ie. BCT1.1)?

Thanks!

Paul

ncborcherding commented 1 year ago

Hey Paul,

All the seurat objects/anndata .h5 objects should follow the naming convention (such as BCT1.1). If you load the seurat object - the orig.ident variable is also using the naming convention. A summary of the sample id/naming convention is actually better described on the dev branch.

Nick

p-gueguen commented 1 year ago

Thanks a lot Nick, that's very clear now. Have a great day.

Paul