Songpeng Zu

@wkl1990 Thank you!

1. It seems that Zenodo needs new doi, instead of the doi from our paper. 2. For NCBI, we'd better change the anndata.tar to three independent h5ad files, and add...

@jcs090218 Thanks for the reply! Following the README, after installing the depencies like Tree-sitter-cli, I can now have the binary files under bin/. But even I change the branch from...

@jcs090218 @meain Thanks for your replies! when i use the old version of tree-sitter, I can now have the latest tree-sitter-r. I did this in a dirty way: go to...

Hi Kai, Thanks for your suggestions! 1. I will give it a look. In MACS2/3, it allows us to shift and extend the fragments, not sure if your function of...

@kaizhang https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.tl.macs3.html From this doc, it supported the unmerged content, like save_bdg. Do you think we should merge this commit or update the document to reflect the stable version? Thanks!...

1. It seems OK now for `to_adata`, but still `a.X `has error. 2. Another question is when I transform it into Ann, the fragment information is lost. Can I also...

@yojetsharma Thank you! From API, it does not mention this. Sincerely, Songpeng

@LeeTibbert Thanks! I will try Discourse. I see lots of activities there, why people use that instead of issues~~~ I will follow your suggestion to give it a try！ Sincerely,...

@LeeTibbert Thank you sooo much for all the detailed responses ! I think you have shown me some valuable resources that I need some time to digest. Before that, I...