Cell Sub-type Annotation

[frankchen121212]

Hi Ruochi,

Thank you for your excellent work in both Higashi and fast-Higashi. I'm currently working with the 4 datasets mentioned in your paper (Lee, Liu, Tan, and Ramani). I noticed that you have created the "label_info.pickle" file, which includes cell subtype information, batch ID, and other annotations for each cell.

However, I couldn't find these annotations in the original GEO accession files. For example, in the Lee et al. dataset, there are cell subtypes like 'L2/3', 'ODC', 'Sst', 'L5', 'Astro', etc. listed in the manuscript, but I can't locate the raw cell subtype information in the raw contacts.txt file or the indexed.tsv file (under each cell sample ID).

Maybe I'm missing something. Your advise will be so helpful. Thank you!