Kai Zhang
Kai Zhang
I will add the docs later. `AnnDataSet` is less powerful than `MuData`, as `AnnDataSet` assumes the underlying anndatas come from homogeneous sources, e.g., same type of experiment, having exactly the...
Sorry for the inconvenience, but the new anndata implementation is necessary for analyzing large datasets. Initially, I didn't appreciate the inconvenience introduced by these changes. Thanks for bringing this up...
I've made good progress in adding in-memory AnnData to SnapATAC2. Please use issue #79 to track the progress.
Update: multiple backend support is now added in [anndata-rs](https://github.com/kaizhang/anndata-rs). This is one step towards supporting the Zarr format in SnapATAC2.
Good idea! Yes, we can add `read_10x_mtx` to the package. Do you want to give it a try?
scanpy is not a mandatory dependency. It would be better not to rely on scanpy for this.
A function called "read_10x_mtx" was added with this commit 1a7f69269514fd9ba4b31c293ca68d0999642782 for reading mtx files generated by 10x genomics. I'm closing this issue now.
Could you please share the h5ad file with me, so that I can try to reproduce the issue?
AnnDataSet provide concatenated view of multiple AnnData objects. You can't combine AnnDataSet objects. AnnDataSet stores links to AnnData objects (h5ad files). To combine several AnnDataSet objects, you can recreate a...
You are using the `concat` function from the anndata package. Please make sure the AnnData objects are read by the `read` function from the anndata package (or in in-memory mode).