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Published 20 hours ago • verified publisher icon kaizhang

SnapATAC2 notebooks to reproduce CATlas results

Open gokceneraslan opened this issue 2 years ago • 3 comments
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I was wondering if there is any notebooks using SnapATAC2 to generate matrices provided on the catlas.org website such as the cell type x CRE matrix or cell type specific peaks.

According to the paper I believe Taiji was the framework used for the analysis but a notebook generating these matrices using the latest SnapATAC2 would be an amazing resource for the community.

Sorry if this already exists but just wanted to ask.

gokceneraslan avatar Feb 25 '23 01:02 gokceneraslan

@gokceneraslan Thanks for this suggestion! This is on my to-do list. I'm working on the SnapATAC2 manuscript. This may be a part of it. Please stay tuned!

kaizhang avatar Feb 27 '23 05:02 kaizhang

Thanks! Looking forward to it.

gokceneraslan avatar Feb 28 '23 21:02 gokceneraslan

@gokceneraslan Maybe you can check my repo firstly: https://github.com/beyondpie/CEMBA_wmb_snATAC/tree/main

beyondpie avatar Nov 22 '23 06:11 beyondpie