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

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity

(2019) Peter van Galen et al.   CELL

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

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

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

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

Landscape of stimulation-responsive chromatin across diverse human immune cells

(2019) Diego Calderon et al.   NATURE GENETICS

Determinants of enhancer and promoter activities of regulatory elements

(2019) Robin Andersson et al.   NATURE REVIEWS GENETICS

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

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

(2018) Carl G. de Boer et al.   BMC BIOINFORMATICS

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

(2018) Jason D. Buenrostro et al.   CELL

Transcript-indexed ATAC-seq for precision immune profiling

(2018) Ansuman T. Satpathy et al.   NATURE MEDICINE

Unsupervised clustering and epigenetic classification of single cells

(2018) Mahdi Zamanighomi 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

The cis-regulatory dynamics of embryonic development at single-cell resolution

(2018) Darren A. Cusanovich et al.   NATURE

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

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

(2017) Maxwell R Mumbach et al.   NATURE GENETICS

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

(2017) Alicia N Schep et al.   NATURE METHODS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

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

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

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE