ArticleScientific reports2020
Comparison of differential accessibility analysis strategies for ATAC-seq data.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 1 of them a synthesis that pooled it.
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Who cites it
46 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Bibliometric Analysis of ATAC-Seq and Its Use in Cancer Biology via Nucleic Acid Detection.Frontiers in medicine · 2020Pooled it
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- cfDECOR: a novel approach for estimating cell type contributions to cfDNA based on chromatin accessibility patterns.Scientific reports · 2026Article
- Integrated chromatin and transcriptomic profiling reveals sex-specific mechanisms of gene regulation in hepatic nutrient responses.PLoS biology · 2026Article
- Improving calls of differentially transcribed enhancers and their upstream regulators.Bioinformatics advances · 2026Article
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- A molecular circuit regulates fate plasticity in emerging and adult AT2 cells.Nature communications · 2025Article
- Polygenic basis of incipient reproductive isolation in hybridizing populations is revealed by pangenomic and epigenetic divergence.bioRxiv : the preprint server for biology · 2025Article
- Lymphoma accelerates T cell and tissue aging.Cancer cell · 2025Article
- Improving confidence of differential transcription calls in enhancers.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive Transcriptomic and Epigenomic Insights into Environmental Toxicant Exposures: The TaRGET II Resource.bioRxiv : the preprint server for biology · 2025Article
- NFIA regulates articular chondrocyte fatty acid metabolism and joint homeostasis.Science translational medicine · 2025Article
- An automated ATAC-seq method reveals sequence determinants of transcription factor dose response in the open chromatin.bioRxiv : the preprint server for biology · 2025Article
- The APOE isoforms differentially shape the transcriptomic and epigenomic landscapes of human microglia xenografted into a mouse model of Alzheimer's disease.Nature communications · 2025Article
- HSV-1 infection induces a downstream shift of the +1 nucleosome.Journal of virology · 2025Article
- Mechanism of expression regulation of head-to-head overlapping protein-coding genes INO80E and HIRIP3.Communications biology · 2025Article
- Application of computational algorithms for single-cell RNA-seq and ATAC-seq in neurodegenerative diseases.Briefings in functional genomics · 2025Review
- Monitoring of single-nucleus chromatin landscape of ischemic stroke in mouse cerebral cortex across time.Scientific data · 2025Article
- Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.Nature neuroscience · 2024Review
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13 authors.
Funding
Abstract
ATAC-seq is widely used to measure chromatin accessibility and identify open chromatin regions (OCRs). OCRs usually indicate active regulatory elements in the genome and are directly associated with the gene regulatory network. The identification of differential accessibility regions (DARs) between different biological conditions is critical in determining the differential activity of regulatory elements. Differential analysis of ATAC-seq shares many similarities with differential expression analysis of RNA-seq data. However, the distribution of ATAC-seq signal intensity is different from that of RNA-seq data, and higher sensitivity is required for DARs identification. Many different tools can be used to perform differential analysis of ATAC-seq data, but a comprehensive comparison and benchmarking of these methods is still lacking. Here, we used simulated datasets to systematically measure the sensitivity and specificity of six different methods. We further discussed the statistical and signal density cut-offs in the differential analysis of ATAC-seq by applying them to real data. Batch effects are very common in high-throughput sequencing experiments. We illustrated that batch-effect correction can dramatically improve sensitivity in the differential analysis of ATAC-seq data. Finally, we developed a user-friendly package, BeCorrect, to perform batch effect correction and visualization of corrected ATAC-seq signals in a genome browser.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.