ArticleGenome biology2021
simATAC: a single-cell ATAC-seq simulation framework.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Inferring tumor absolute copy number and clonal substructure from single-cell chromatin accessibility.Briefings in bioinformatics · 2026Article
- Computational Analyses and Challenges of Single-cell ATAC-seq.Genomics, proteomics & bioinformatics · 2025Review
- scCirclehunter delineates ecDNA-containing cells using single-cell ATAC-seq, with a focus on glioblastoma.Cell discovery · 2025Article
- reDA: differential abundance testing on scATAC-seq data using random walk with restart.Bioinformatics (Oxford, England) · 2025Article
- simPIC:flexible simulation of paired-insertion counts for single-cell ATAC sequencing data.bioRxiv : the preprint server for biology · 2025Article
- scMultiSim: simulation of single-cell multi-omics and spatial data guided by gene regulatory networks and cell-cell interactions.Nature methods · 2025Article
- The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments.Research square · 2025Article
- The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments.bioRxiv : the preprint server for biology · 2025Article
- Detecting copy-number alterations from single-cell chromatin sequencing data by AtaCNA.Cell reports methods · 2025Article
- Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information.BMC bioinformatics · 2023Article
- A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing.PLoS computational biology · 2023Article
- scIBD: a self-supervised iterative-optimizing model for boosting the detection of heterotypic doublets in single-cell chromatin accessibility data.Genome biology · 2023Article
- simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data.Bioinformatics (Oxford, England) · 2023Article
- scChIX-seq infers dynamic relationships between histone modifications in single cells.Nature biotechnology · 2023Article
- Clustering single-cell multimodal omics data with jrSiCKLSNMF.Frontiers in genetics · 2023Article
- TooManyPeaks identifies drug-resistant-specific regulatory elements from single-cell leukemic epigenomes.Cell reports · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) identifies regulated chromatin accessibility modules at the single-cell resolution. Robust evaluation is critical to the development of scATAC-seq pipelines, which calls for reproducible datasets for benchmarking. We hereby present the simATAC framework, an R package that generates scATAC-seq count matrices that highly resemble real scATAC-seq datasets in library size, sparsity, and chromatin accessibility signals. simATAC deploys statistical models derived from analyzing 90 real scATAC-seq cell groups. simATAC provides a robust and systematic approach to generate in silico scATAC-seq samples with known cell labels for assessing analytical pipelines.
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Registered trials
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.