ArticleGenome biology2020
scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers, 1 of them a synthesis that pooled it.
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Who cites it
49 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
- scGSI: Graph-guided self-supervised integration of paired single-cell multi-omics.PLoS computational biology · 2026Article
- A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.Cell reports. Medicine · 2026Article
- Single-cell chromatin accessibility and cis-regulatory element analyses in plants using the scPlantReg platform.Nature plants · 2026Article
- Spatial Transcriptomics Unveils the Blueprint of Mammalian Lung Development.Genomics, proteomics & bioinformatics · 2026Article
- A pipeline for single-cell chromatin accessibility data analysis.Blood science (Baltimore, Md.) · 2026Article
- Advances in scCUT&Tag and computational analysis for single-cell gene regulatory element mapping.Briefings in bioinformatics · 2026Review
- Decoding cnidarian cell type gene regulation.Nature ecology & evolution · 2026Article
- Computational Analyses and Challenges of Single-cell ATAC-seq.Genomics, proteomics & bioinformatics · 2025Review
- Recent advances in single-cell bioinformatics for inferring higher-order chromatin contact maps.BMB reports · 2025Review
- Assessment and applications of joint profiling of single-cell chromatin accessibility and transcriptome.Briefings in bioinformatics · 2025Review
- IMATAC imputes single-cell ATAC-seq data by deep hierarchical network with denoising autoencoder.Briefings in bioinformatics · 2025Article
- Integrating Artificial Intelligence in Next-Generation Sequencing: Advances, Challenges, and Future Directions.Current issues in molecular biology · 2025Review
- HDAC4 Inhibits NMDA Receptor-mediated Stimulation of Neurogranin Expression.Molecular neurobiology · 2025Article
- DeepExDC interprets genomic compartmentalization changes in single-cell Hi-C data.Briefings in bioinformatics · 2025Article
- Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiring.Nature genetics · 2025Article
- Native stem cell transcriptional circuits define cardinal features of high-risk leukemia.The Journal of experimental medicine · 2025Article
- Capturing cell-type-specific activities of cis-regulatory elements from peak-based single-cell ATAC-seq.Cell genomics · 2025Article
- Application of computational algorithms for single-cell RNA-seq and ATAC-seq in neurodegenerative diseases.Briefings in functional genomics · 2025Review
- A cell atlas of the human fallopian tube throughout the menstrual cycle and menopause.Nature communications · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Single-cell chromatin accessibility sequencing has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. However, there is a lack of open-source software for comprehensive processing, analysis, and visualization of such data generated using all existing experimental protocols. Here, we present scATAC-pro for quality assessment, analysis, and visualization of single-cell chromatin accessibility sequencing data. scATAC-pro computes a range of quality control metrics for several key steps of experimental protocols, with a flexible choice of methods. It generates summary reports for both quality assessment and downstream analysis. scATAC-pro is available at https://github.com/tanlabcode/scATAC-pro.
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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.