Published on Fri Sep 10 2021

scBasset: Sequence-based modeling of single cell ATAC-seq using convolutional neural networks

Yuan, H., Kelley, D. R.

Single cell ATAC-seq shows great promise for studying cellular heterogeneity in epigenetic landscapes. There remain significant challenges in the analysis of scATAC data due to the inherent high dimensionality and sparsity. Here we introduce scBasset, a sequence-based convolutional neural network

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Abstract

Single cell ATAC-seq (scATAC) shows great promise for studying cellular heterogeneity in epigenetic landscapes, but there remain significant challenges in the analysis of scATAC data due to the inherent high dimensionality and sparsity. Here we introduce scBasset, a sequence-based convolutional neural network method to model scATAC data. We show that by leveraging the DNA sequence information underlying accessibility peaks and the expressiveness of a neural network model, scBasset achieves state-of-the-art performance across a variety of tasks on scATAC and single cell multiome datasets, including cell type identification, scATAC profile denoising, data integration across assays, and transcription factor activity inference.