How to use ATAC dataset

LiuLab-Bioelectronics-Harvard / UnitedNet

GNU General Public License v3.0

38 stars 14 forks source link

How to use ATAC dataset #9

Open Layne-Huang opened 10 months ago

Layne-Huang commented 10 months ago

Hi,

Thanks for your excellent work. I have downloaded the multiome ATAC + gene expression BMMCs dataset under accession code “GSE194122”. However, I could not find the atac_processed.h5ad and gex_processed.h5ad from a single file GSE194122_openproblems_neurips2021_multiome_BMMC_processed.h5ad in the ATAC related jupyter notebooks. Could you please help me solve it?

Thanks.

xintangg commented 9 months ago

Hi Layne

Sorry, I was not checking this repository recently. The data availability has been described in the "Data Availability" section of our paper: https://www.nature.com/articles/s41467-023-37477-x

Let me know if you have difficulty accessing them and I am happy to help.

Thanks

AnthonyShea1 commented 6 months ago

More specifically, the Zenodo data entry holds the files you want to use.

https://zenodo.org/records/7708592#.ZBSIp3Yo9aQ