Songpeng Zu
Songpeng Zu
Sure. I see `scanpy` is also our dependence. I can basically call scancp's function, which load data into memory, then create SnapATAC2's AnnData to store it in file. What do...
Thanks, Kai! Sorry for the late response, I am now in the job market...
Hi Kai @kaizhang , I would suggest we copy the behavior of getting gene symbols by default in scanpy.read_10x_mtx (https://github.com/scverse/scanpy/blob/214e05bdc54df61c520dc563ab39b7780e6d3358/scanpy/readwrite.py#L570): ``` genes = pd.read_csv( path / f"{prefix}{'genes' if is_legacy else...
@kaizhang I think I can add one R script for this task. Do you have any suggestions about adding a Rscript to this repo? I know rpy2 can call R...
Hi Kai, I now have one single-file script for this: https://github.com/beyondpie/tools/blob/main/singlecell/SnapATACAnnData2Seurat.R I still need some time to test it. Do you think we can put it somewhere in this repo...
Another potential function, should be convert SnapATAC2 AnnData to Signac object?
@lf96abc No. I haven't used Signac before. And probably will give it a try later.
@gokceneraslan Maybe you can check my repo firstly: https://github.com/beyondpie/CEMBA_wmb_snATAC/tree/main
@kaizhang Thanks! 1. Do you think we can add this to your document? For example, here: https://kzhang.org/epigenomics-analysis/anndata.html. 2. Is this related with the implementation in Rust. I don't know why...
@wkl1990 Kangli, do you have that code or you publish it already?