ScATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting.

ABSTRACT: Single-cell ATAC-seq (scATAC-seq) is a recently developed approach that provides means to investigate open chromatin at single cell level, to assess epigenetic regulation and transcription factors binding landscapes. The sparsity of the scATAC-seq data calls for imputation. Similarly, preprocessing (filtering) may be required to reduce computational load due to the large number of open regions. However, optimal strategies for both imputation and preprocessing have not been yet evaluated together. We present SAPIEnS (scATAC-seq Preprocessing and Imputation Evaluation System), a benchmark for scATAC-seq imputation frameworks, a combination of state-of-the-art imputation methods with commonly used preprocessing techniques. We assess different types of scATAC-seq analysis, i.e. clustering, vis

SUBMITTER: Akhtyamov P 

PROVIDER: S-EPMC10714317 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature