Songpeng Zu

Hi Kai, I used Yang Li's previous non-negative matrix factorization (nmf) pipeline (with some modifications by myself) to analyze the modules for pseudo-bulk level cell-by-peak matrix. https://github.com/beyondpie/CEMBA_wmb_snATAC/tree/main/04.nmf Do you think...

Hi there, This is really a fantastic package, and I am now using it everyday. One problem I now have is that, once I open the format-all mode, it will...

Add store_bdg, SPMR, broad parameters for calling peaks using MACS3

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Hi Kai, I add three parameters for peak calling. 1. On bed graph generation: - SPMR and store_bdg, I open the two parameters since we notice that MACS2/3 can generate...

AnnDataSet can not be converted to AnnData when the X is empty

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Hi Kai, I have several AnnData created directly from fragment files. If I did not add any matrix to AnnData's X, and combine them into AnnDataSet (this step is OK)....

Hi Hanqing, Thanks for the great package! When I use the integration module, I find it will report error when I plan to save it using `SeuratIntegration.save` with parameter `save_adata=True`....

list the codes and data about how we generate the figures.

Ref: https://github.com/AllenInstitute/abc_atlas_access