4.8 Article

EpiScanpy: integrated single-cell epigenomic analysis

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

Rongxin Fang et al.

Summary: The paper introduces SnapATAC, a software package for analyzing single cell ATAC-seq datasets, which can dissect cellular heterogeneity and map cellular states' trajectories. The Nystrom method allows processing data from up to a million cells, and it incorporates existing tools for single cell ATAC-seq dataset analysis. SnapATAC is applied to mouse secondary motor cortex profiles and identifies candidate regulatory elements and cell-type specific transcriptional regulators.

NATURE COMMUNICATIONS (2021)

Article Biotechnology & Applied Microbiology

scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution

Chantriolnt-Andreas Kapourani et al.

Summary: High-throughput single-cell measurements of DNA methylomes reveal the role of methylation heterogeneity in gene regulation. The hierarchical Bayesian model scMET addresses technical limitations, quantifies biological heterogeneity, identifies highly variable epigenetic features, and facilitates the characterization of epigenetically distinct cell populations.

GENOME BIOLOGY (2021)

Article Multidisciplinary Sciences

A human cell atlas of fetal chromatin accessibility

Silvia Domcke et al.

SCIENCE (2020)

Article Biotechnology & Applied Microbiology

Integrative analyses of single-cell transcriptome and regulome using MAESTRO

Chenfei Wang et al.

GENOME BIOLOGY (2020)

Review Genetics & Heredity

Integrative single-cell analysis

Tim Stuart et al.

NATURE REVIEWS GENETICS (2019)

Article Biochemical Research Methods

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data

Carmen Bravo Gonzalez-Blas et al.

NATURE METHODS (2019)

Article Biochemistry & Molecular Biology

Comprehensive Integration of Single-Cell Data

Tim Stuart et al.

Article Biochemistry & Molecular Biology

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

Joshua D. Welch et al.

Article Biotechnology & Applied Microbiology

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

Ansuman T. Satpathy et al.

NATURE BIOTECHNOLOGY (2019)

Article Biochemical Research Methods

Fast, sensitive and accurate integration of single-cell data with Harmony

Ilya Korsunsky et al.

NATURE METHODS (2019)

Article Multidisciplinary Sciences

SCALE method for single-cell ATAC-seq analysis via latent feature extraction

Lei Xiong et al.

NATURE COMMUNICATIONS (2019)

Article Biochemical Research Methods

A discriminative learning approach to differential expression analysis for single-cell RNA-seq

Vasilis Ntranos et al.

NATURE METHODS (2019)

Article Biochemistry & Molecular Biology

Classifying cells with Scasat, a single-cell ATAC-seq analysis tool

Syed Murtuza Baker et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biotechnology & Applied Microbiology

Assessment of computational methods for the analysis of single-cell ATAC-seq data

Huidong Chen et al.

GENOME BIOLOGY (2019)

Article Biotechnology & Applied Microbiology

Melissa: Bayesian clustering and imputation of single-cell methylomes

Chantriolnt-Andreas Kapourani et al.

GENOME BIOLOGY (2019)

Article Biochemical Research Methods

BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization

Carl G. de Boer et al.

BMC BIOINFORMATICS (2018)

Article Multidisciplinary Sciences

Unsupervised clustering and epigenetic classification of single cells

Mahdi Zamanighomi et al.

NATURE COMMUNICATIONS (2018)

Article Biochemistry & Molecular Biology

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

Darren A. Cusanovich et al.

Article Biochemistry & Molecular Biology

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

Hannah A. Pliner et al.

MOLECULAR CELL (2018)

Article Biotechnology & Applied Microbiology

SCANPY: large-scale single-cell gene expression data analysis

F. Alexander Wolf et al.

GENOME BIOLOGY (2018)

Article Biochemical Research Methods

chromVAR : inferring transcription-factor-associated accessibility from single-cell epigenomic data

Alicia N. Schep et al.

NATURE METHODS (2017)

Article Biochemical Research Methods

Single-cell regulome data analysis by SCRAT

Zhicheng Ji et al.

BIOINFORMATICS (2017)

Article Biotechnology & Applied Microbiology

DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning

Christof Angermueller et al.

GENOME BIOLOGY (2017)

Article Biochemical Research Methods

Diffusion pseudotime robustly reconstructs lineage branching

Laleh Haghverdi et al.

NATURE METHODS (2016)

Article Multidisciplinary Sciences

Single-cell chromatin accessibility reveals principles of regulatory variation

Jason D. Buenostro et al.

NATURE (2015)

Article Biochemical Research Methods

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

Sebastien A. Smallwood et al.

NATURE METHODS (2014)

Article Mechanics

Fast unfolding of communities in large networks

Vincent D. Blondel et al.

JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT (2008)

Article Biotechnology & Applied Microbiology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang et al.

GENOME BIOLOGY (2008)