IMATAC imputes single-cell ATAC-seq data by deep hierarchical network with denoising autoencoder.

ABSTRACT: Single-cell ATAC-seq (scATAC-seq) technology allows the interrogation of chromatin accessibility of individual cells. Dropout events occur while the sequencing data signals at some bona fide chromatin sites of individuals are not captured, and the curse of these dropouts in scATAC-seq data inevitably hinders downstream analysis. It remains a challenge to impute scATAC-seq data due to its high dimensionality, sparsity, and near-binarization properties. Herein, we propose IMATAC, a deep hierarchical network with denoising autoencoder for imputing scATAC-seq data in the form of peak by cell. The network embeds scATAC-seq data into a latent space by a deep hierarchical architecture at two different levels, including bottom level for local details and top level for global information, that help

SUBMITTER: Li Y 

PROVIDER: S-EPMC12478030 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature