search

JackieHanLab / TOSICA

Transformer for One-Stop Interpretable Cell-type Annotation
MIT License
126 stars 24 forks source link

Questions about reading certain datasets #8

Closed HelloWorldLTY closed 1 year ago

HelloWorldLTY commented 1 year ago

Hi, I look for some datasets you used in this paper and for one particular datasets,GSE1159677, I find some errors when I intend to use read_h5f based on either scanpy or pandas.

image

By using sc.read_10x_h5

Did you use seurat to read this file? I think the problem is caused by the sparse or storage. The count information here is a one d vector. Thanks a lot.

JackieHanLab commented 1 year ago

For data GSE159677, we downloaded the 10X featurebcmatrixfiltered.tar files in the GSE159677_RAW.tar, and used Seurat for their pre-processing.