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quadbio / organoid_regulomes

Reproducibility code for the manuscript: 'Inferring and perturbing cell fate regulomes in human cerebral organoids
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Data release request | velocity_graph reproducibility #3

Open ilibarra opened 5 months ago

ilibarra commented 5 months ago

@joschif thank you for the code and data release!

I am trying to find the unspliced/spliced counts for RNA_data.h5ad, or related trajectory data files for scVelo. Were those files listed somewhere in Zenodo? If not released, may those be provided somehow for complementing the main RNA_ATAC_metacells_srt data release? https://zenodo.org/records/7687749

I am mainly looking to rebuild the velocity graph information from 4b? I understand there's an output file with some velo_graphs saved. That can also be very useful, if a way to rebuild from the data release is possible, or directly made available as a set of parallel h5ad files. Thank you! https://github.com/quadbio/organoid_regulomes/blob/main/trajectory/velocity_cellrank.py#L18 https://github.com/quadbio/organoid_regulomes/blob/main/trajectory/velocity_cellrank.py#L41 image

joschif commented 3 months ago

Sorry for the late reply, I've kindof missed this. I'll look for the h5ad.

joschif commented 3 months ago

The h5ad which the velocities are computed from and stored in should be here: https://drive.google.com/file/d/1wrWyf7V0EUZxQt9ur55Mu7Q8OHFV8JLX/view?usp=sharing