SnapATAC2
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kaizhang
Single-cell epigenomics analysis tools
SnapATAC2 uses the backed AnnData to save memory and speed up the processing of large files. But for small datasets, the backed AnnData is less convenient to work with than...
Hi Dr.Zhang, I am working on paired-tag data and as recommended, trying to analyze paired-tag DNA sequencing data using snapATAC. I wonder how I can load the results of paired-tag...
The latest update with the new anndata implemetations seems to make data subsetting much more inconvenient. For example, when I want to try out different quality control filtering critiria(let's say...
- [ ] Improve the API documentation - [ ] Add descriptions of the algorithms used in the package
Are there any docs available for the `AnnDataSet` class? I couldn't find a page in the docs. AFAICT, it looks quite like a [MuData](https://mudata.readthedocs.io/en/latest/) object, in that it has top...
## 1: Make similarity matrix calculation more time- and space-efficient We can use the approximate nearest neighbor search to speed up and sparsify the graph Laplacian. Here are some good...
Thank you for developing this tool. SnapATAC2 version: 2.5.3 I have a set of fragment files with a matching set of whitelisted barcodes files (the whitelisting was done via other...
Hi Kai, Here is the description of filter features: ``` If inplace = False, return a boolean index mask that does filtering, where True means that the feature is kept,...
Hi, I ran into error when running ```python net = snap.tl.init_network_from_annotation(regions, anno_file =snap.genome.hg38, upstream = 250000, downstream= 250000, id_type = 'gene_name', coding_gene_only = True) net = snap.tl.add_cor_scores(net, gene_mat=gene_mat, peak_mat=peak_mat, select=None,...
