ArticleNature methods2024
Modeling fragment counts improves single-cell ATAC-seq analysis.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- What-if effects: A tale of entangled covariates.Patterns (New York, N.Y.) · 2026Article
- Disentangling covariate effects on single-cell-resolved epigenomes with DeepDive.Patterns (New York, N.Y.) · 2026Article
- SC-framework: A robust and FAIR semi-interactive environment for single-cell resolution datasets.iScience · 2026Article
- Consensus Pituitary Atlas, a scalable resource for annotation, novel marker discovery, and analyses in mouse pituitary gland research.Cell reports · 2026Article
- ArchVelo: archetypal velocity modeling for single-cell multi-omic trajectories.Nature communications · 2026Article
- Organ-Specific and Conserved Regulatory Logic Orchestrates Gene Expression in the Embryonic Mesothelium.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Cross-modality representation and multi-sample integration of spatially resolved omics data.Briefings in bioinformatics · 2026Article
- PAIR: Reconstructing Single-Cell Open-Chromatin Landscapes for Transcription Factor Regulome Mapping.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- ModelingbioRxiv : the preprint server for biology · 2026Article
- A comprehensive benchmarking study on computational tools for cross-omics label transfer from single-cell RNA to ATAC data.G3 (Bethesda, Md.) · 2026Article
- Single-nucleus multiome analysis in the human prefrontal cortex identifies gene expression and cis-regulatory elements associated with aging.Cell reports · 2026Article
- Systematic evaluation of single-cell multimodal data integration enhances cell type resolution and discovery of clinically relevant states in complex tissues.Genome biology · 2026Article
- iAODE for benchmarking and continuum modeling of single-cell chromatin accessibility.Communications biology · 2026Article
- CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data.Bioinformatics (Oxford, England) · 2026Article
- Benchmarking LLM-based agents for single-cell omics analysis.Genome biology · 2026Article
- Advances in scCUT&Tag and computational analysis for single-cell gene regulatory element mapping.Briefings in bioinformatics · 2026Review
- Article
- scCCVGBen for benchmarking of single-cell representation learning anchored on a centroid-coupled variational graph attention autoencoder across scRNA-seq and scATAC-seq.Frontiers in genetics · 2026Article
- scooby: modeling multimodal genomic profiles from DNA sequence at single-cell resolution.Nature methods · 2025Article
- Single-Cell Multi-Modal Differential Analysis of the Human Neo-Cortex in HIV Infection Reveals Similarities with Hallmarks of Alzheimer's Disease.Research square · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Single-cell ATAC sequencing coverage in regulatory regions is typically binarized as an indicator of open chromatin. Here we show that binarization is an unnecessary step that neither improves goodness of fit, clustering, cell type identification nor batch integration. Fragment counts, but not read counts, should instead be modeled, which preserves quantitative regulatory information. These results have immediate implications for single-cell ATAC sequencing analysis.
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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.