Single-cell chromatin state analysis with Signac

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

Spatially mapped single-cell chromatin accessibility

(2021) Casey A. Thornton et al.   Nature Communications

Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq

(2021) Elliott Swanson et al.   eLife

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

(2021) Eleni P. Mimitou et al.   NATURE BIOTECHNOLOGY

EpiScanpy: integrated single-cell epigenomic analysis

(2021) Anna Danese et al.   Nature Communications

High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer

(2021) Sarah E. Pierce et al.   Nature Communications

Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility

(2020) Qiao Rui Xing et al.   GENOME RESEARCH

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

(2020) Caleb A. Lareau et al.   NATURE BIOTECHNOLOGY

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase

(2020) Janne Purhonen et al.   NUCLEIC ACIDS RESEARCH

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

(2020) Sai Ma et al.   CELL

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification

(2019) Wai Lim Ku et al.   NATURE METHODS

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

(2019) Leif S. Ludwig et al.   CELL

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

(2019) Carmen Bravo González-Blas et al.   NATURE METHODS

Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA

(2019) Jin Xu et al.   eLife

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

(2019) Caleb A. Lareau et al.   NATURE BIOTECHNOLOGY

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

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

Profiling chromatin states using single-cell itChIP-seq

(2019) Shanshan Ai et al.   NATURE CELL BIOLOGY

CoBATCH for High-Throughput Single-Cell Epigenomic Profiling

(2019) Qianhao Wang et al.   MOLECULAR CELL

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome

(2019) Chenxu Zhu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq)

(2019) Benjamin Carter et al.   Nature Communications

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Detection and removal of barcode swapping in single-cell RNA-seq data

(2018) Jonathan A. Griffiths et al.   Nature Communications

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

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

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks

(2018) Adam J. Rubin et al.   CELL

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

(2018) Syed Murtuza Baker et al.   NUCLEIC ACIDS RESEARCH

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

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

(2017) Alicia N Schep et al.   NATURE METHODS

Dr.seq2: A quality control and analysis pipeline for parallel single cell transcriptome and epigenome data

(2017) Chengchen Zhao et al.   PLoS One

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Identifying Causal Variants at Loci with Multiple Signals of Association

(2014) F. Hormozdiari et al.   GENETICS

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

(2014) Sébastien A Smallwood et al.   NATURE METHODS

A smart local moving algorithm for large-scale modularity-based community detection

(2013) Ludo Waltman et al.   EUROPEAN PHYSICAL JOURNAL B

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

Sequences and consequences

(2009) S. Brenner   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES