SnapATAC2
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kaizhang
Single-cell epigenomics analysis tools
Hey Kai, Running into an error when using the `export_coverage` function with mostly defaults: ```python import snapatac2 as snap print(snap.__version__) # 2.5.2 adata = snap.read( "clustered.h5ad", backed="r+" ) snap.ex.export_coverage( adata=adata,...
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...
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](http://yed.ucsd.edu:8787/cCRE_by_cell_type/) matrix or cell type specific...
Hi, Thank you for developing this nice tool. I am trying to follow the pipline of Atlas-scale Analysis.And I am trying to add the raw metadata provided in the paper...
Greetings, I am relatively new to atac-seq analysis and I was wondering, why is the groupby parameter obligatory in the macs3 peak calling function? I took a subset of cells...
- [x] add an option to filter peaks based on blacklist. - [ ] provide additional peak filtering/correction methods, such as the score per million correction. - [x] call reproducible...
Hi Kai, Love all the utilities you provide for generating fragments file (especially it supports single-end data like Paired-Tag) and count matrix. I wonder whether you think would be useful...
When the input is a sparse array, the `.chunk_X()` function in anndata package still returns a dense array instead of a sparse array. This will result in out-of-memory errors for...
I have non-single cell ATAC-seq data, can I use SnapATAC2 to analyse it?
