---
# System prepended metadata

title: '2022-05-10: Isaac + Kai – snapatac2 anndata-rs'
tags: [' meeting', ' anndata', scverse, ' atac-seq']

---

---
tags: scverse, meeting, atac-seq, anndata
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# 2022-05-10: Isaac + Kai – snapatac2 anndata-rs

*Attendees:*

## Agenda

* scverse
* snapatac2 and atac-seq in python
* anndata-rs
    * Scope/ plans
    * Zarr (and cloud friendly formats)
    * Tensors and arrow
    * Polars and datafusion
* anndata and anndata-rs
    * Compatibility
    * anndata-rs AnnDataset as a special case of MuData?

## Notes

* Kai Bin Ruan lab in san diego
* scverse Qs
    * would be interested in having his lab involved

### snapatac2

* Scalable tools for end to end single celll epigenomics data
* Does not alignment
    * preprocessing
    * dimension reduction
        * Others: rsi
    * Want
        * Base pair resolution **Qs** not bins?
        * Eventually generate base pair resolution
        * Lazily read X (since base pair resolution is memory hungry)
    * Focus
        * Accuracy
        * Scalability
    * Dimension reduction
        * typically tf-idf -> svd
        * instead uses spectral embedding
            * Create similarity matrix, but an approximate one
            * Flexible similarity metrics
    * Use peaks when they are present
    * subsampling then clustering ARI?
    * Collaborate with Allen on single cell brain dataset
    * Comparison with archr – preprocessing
        * Fragments file – tabix bed file
            * archr
    * anndata-rs
* anndata-rs
    * Would like a more mature anndata-specification
    * Dask
    * AnnCollection is 
* Batch effects
    * Across labs not great
    * Between samples is okay
    * Integration
        * Harmony
        * Patched mnnpy
        * Calling peaks on the merged data
* Interest in regulatory genomics
    * multiome
    * Assoicating regions with peaks
* mudata + muon
    * muon.atac
        * Being involved in snapatac2
        * Scope for snapatac2 involves regulatory genomics
        * Ignacio connects
    * zarr


### Follow up

* Short term
    * Isaac will connect Kai with Ignacio
    * Kai will let Isaac know what needs more specification
* Long term
    * How can we make a single good genomic regions library?
    * Regulatory genomics related metadata
