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included PBMC paired data
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kimmo1019 committed Nov 17, 2020
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![model](https://github.com/kimmo1019/scDEC/blob/master/model.png)

scDEC is a computational tool for single cell ATAC-seq data analysis with deep generative neural networks. scDEC enables simultaneously learning the deep embedding and clustering of the cells in an unsupervised manner.
scDEC is a computational tool for single cell ATAC-seq data analysis with deep generative neural networks. scDEC enables simultaneously learning the deep embedding and clustering of the cells in an unsupervised manner. scDEC is also applicable to multi-modal single cell data. We tested it on the PBMC paired data (scRNA-seq and scATAC-seq) from 10x Genomics (see Tutorials).

## Requirements
- TensorFlow==1.13.1
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[Tutorial Full mouse atlas](https://github.com/kimmo1019/scDEC/wiki/Full-Mouse-atlas) Run scDEC on full Mouse atlas dataset (k=40, 81173 cells)

[Tutorial PBMC10k paired data ](https://github.com/kimmo1019/scDEC/wiki/PBMC10k) Run scDEC on PBMC data, which contains around 10k cells with both scRNA-seq and scATAC-seq (labels were manually annotated from 10x Genomic R&D group)

## Contact

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