ArticleNature communications2021
EpiScanpy: integrated single-cell epigenomic analysis.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers, 2 of them syntheses that pooled it.
What it found
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Who cites it
86 citing papers in PubMed, 2 syntheses or guidelines pooled it, 137 citations in OpenAlex.
- Pooled it
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
- SMORE: joint dimension reduction and cell population discovery on single-cell methylome data.bioRxiv : the preprint server for biology · 2026Article
- DiTSim: A Diffusion-Transformers Based Single-Cell ATAC-seq Data Simulator.Interdisciplinary sciences, computational life sciences · 2026Article
- Integrative Epigenomics: Bioinformatics Strategies for Multi-Omics Data Analysis in Health and Disease.Epigenomes · 2026Review
- SC-framework: A robust and FAIR semi-interactive environment for single-cell resolution datasets.iScience · 2026Article
- Cross-Modal Denoising and Integration of Spatial Multi-Omics Data with CANDIES.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- SpaDC enables sequence-based integrative analysis and regulatory inference of spatial chromatin accessibility data.Communications biology · 2026Article
- Dissecting epigenetic heterogeneity in single-cell DNA methylomes with a unified framework.Nature communications · 2026Article
- Geometry-aware graph attention networks to explain single-cell chromatin states and gene expression with SEAGALL.Genome biology · 2026Article
- High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND.Genome research · 2026Article
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs.Nature neuroscience · 2026Article
- Exploring single-cell and multi-omics technologies and their role in unraveling tumor heterogeneity of hepatocellular carcinoma.Journal of liver cancer · 2026Review
- scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment.Genome research · 2026Article
- A guide to transcriptomic deconvolution in cancer.Nature reviews. Cancer · 2026Review
- Aligned cross-modal integration and regulatory heterogeneity characterization of single-cell multiomic data with deep contrastive learning.Genome medicine · 2026Article
- Developing a comprehensive database and search tool for single-cell ATAC-seq data.Scientific reports · 2026Article
- scRiskDB: a single-cell epigenomic resource linking complex traits to regulatory mechanisms across human tissues.Database : the journal of biological databases and curation · 2026Article
- Computational Analyses and Challenges of Single-cell ATAC-seq.Genomics, proteomics & bioinformatics · 2025Review
26 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
EpiScanpy is a toolkit for the analysis of single-cell epigenomic data, namely single-cell DNA methylation and single-cell ATAC-seq data. To address the modality specific challenges from epigenomics data, epiScanpy quantifies the epigenome using multiple feature space constructions and builds a nearest neighbour graph using epigenomic distance between cells. EpiScanpy makes the many existing scRNA-seq workflows from scanpy available to large-scale single-cell data from other -omics modalities, including methods for common clustering, dimension reduction, cell type identification and trajectory learning techniques, as well as an atlas integration tool for scATAC-seq datasets. The toolkit also features numerous useful downstream functions, such as differential methylation and differential openness calling, mapping epigenomic features of interest to their nearest gene, or constructing gene activity matrices using chromatin openness. We successfully benchmark epiScanpy against other scATAC-seq analysis tools and show its outperformance at discriminating cell types.
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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.