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Published 20 hours ago • verified publisher icon dpeerlab

Accessing cell type labels

Open mbernste opened this issue 4 years ago • 1 comments

Hi,

This work is very interesting and thank you for making these data publicly available!

I am very interested in exploring this dataset, but am having a bit of difficulty.

Specifically, I am having trouble finding where the cell type annotations are stored. I am able to access the counts matrices via the GEO file (file GSE123904_RAW.tar located at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123904 ); however, these matrices do not seem to contain the cell type labels as inferred via the methods described in your publication.

I also downloaded the HDF5 file located at (https:// s3.amazonaws.com/dp-lab-data-public/lung-development-cancer-progression/ PATIENT_LUNG_ADENOCARCINOMA_ANNOTATED.h5 ; however, I am having a hard time interpreting its contents especially in regards to how it relates to the matrices in the GEO entry.

Any help you could provide in accessing the cell type labels for each row in the GEO matrices would be greatly appreciated!

Thanks, Matt

mbernste avatar Mar 17 '20 20:03 mbernste