scATAC-seq

Supervised classification enables rapid annotation of cell atlases

Garnett enables rapid cell type annotation in scRNA-seq and scATAC-seq data using a hierarchical markup language of cell type-specific genes.

scBFA: modeling detection patterns to mitigate technical noise in large-scale single cell genomics data

scBFA mitigates technical noise in single cell genomics data by analyzing detection patterns instead of quantification measurements, improving cell type identification and trajectory inference.

genesorteR: Feature Ranking in Clustered Single Cell Data

genesorteR ranks features in single cell data to identify marker genes more accurately and efficiently than differential expression analysis.

CoBATCH for high-throughput single-cell epigenomic profiling

CoBATCH enables high-throughput single-cell profiling of chromatin-binding proteins by combining combinatorial barcoding with targeted chromatin release, achieving high signal-to-noise and efficient epigenetic analysis.

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

The paper uses scATAC-seq to analyze chromatin accessibility in immune cell development and tumor microenvironments, identifying regulatory elements and trajectories associated with cell differentiation and therapy response.

Linking transcriptome and chromatin accessibility in nanoliter droplets for single-cell sequencing

The paper introduces SNARE-seq, a droplet-based method for simultaneous transcriptome and chromatin accessibility profiling in single cells, and applies it to study neurogenesis in mouse cerebral cortices.

Comprehensive integration of single cell data

Seurat v3 finds scored mutual-nearest-neighbor anchors in canonical correlation space to integrate scRNA-seq batches and transfer labels, protein levels and transcriptome-wide expression across modalities.

Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis

The paper introduces an improved single-cell ATAC-seq method, scip-ATAC-seq, which enhances chromatin dynamics analysis in human corticogenesis organoids.

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data

STREAM is an interactive pipeline for reconstructing and visualizing complex branching trajectories from single-cell transcriptomic and epigenomic data.

Droplet-based combinatorial indexing for massive scale single-cell epigenomics

The paper introduces a droplet-based combinatorial indexing method for high-throughput scATAC-seq, enabling large-scale single-cell chromatin accessibility profiling in mouse and human cells.

clonealign: statistical integration of independent single-cell RNA & DNA-seq from human cancers

clonealign integrates single-cell RNA and DNA sequencing data from cancer samples to identify clone-specific gene expression patterns and dysregulated pathways.

Single cell ATAC-seq identifies broad changes in neuronal abundance and chromatin accessibility in Down Syndrome

The paper uses sci-ATAC-seq to analyze cortical cells in Ts65Dn mice, finding reduced excitatory neurons and increased interneurons, along with changes in chromatin accessibility related to transcription factors.

Destin: toolkit for single-cell analysis of chromatin accessibility

Destin is a framework for analyzing scATAC-seq data, outperforming existing methods in clustering and identifying cell type-specific associations with schizophrenia GWAS loci.

Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

The paper introduces scCAT-seq, a method to simultaneously assay chromatin accessibility and transcriptome in single cells, and demonstrates its application in human pre-implantation embryos to reveal regulatory heterogeneity.

A Bayesian approach for correcting Tn5 transposition bias in ATAC-seq footprinting

The paper corrects Tn5 transposition bias in ATAC-seq to improve footprinting accuracy by using existing tools and a novel global occupancy estimate.

Sparse functional data analysis accounts for missing information in single-cell epigenomics

The paper develops a method to handle sparse data in single-cell epigenomics using functional data analysis, improving coverage estimation for chromatin accessibility.

Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks

Perturb-ATAC combines CRISPR perturbations with single-cell ATAC-seq to identify gene regulatory networks in human cells.

A rapid and robust method for single cell chromatin accessibility profiling

Upfront bulk Tn5 tagging then single-nucleus sorting into plates gives scATAC-seq libraries with higher complexity than Fluidigm C1, resolving 12 clusters among 3,385 mouse splenocytes.

Single cell RNA-seq and ATAC-seq indicate critical roles of Isl1 and Nkx2-5 for cardiac progenitor cell transition states and lineage settlement

The paper uses single-cell RNA-seq and ATAC-seq to study cardiac progenitor cell fate transitions, identifying roles for Isl1 and Nkx2-5 in lineage commitment and gene regulatory networks.

Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity

The paper introduces Pi-ATAC, a method combining single-cell chromatin and proteomic profiling, revealing hypoxia's role in shaping the regulome in tumor cells.

A Universal Algorithm to Detect Rare or Novel Cell Types in High-Throughput Single-Cell Gene Expression Data

The paper introduces an algorithm to detect rare or novel cell types in single-cell gene expression data and identifies a putative new hippocampal cell type.

Classifying cells with Scasat - a tool to analyse single-cell ATAC-seq

The paper introduces Scasat, a pipeline for analyzing single-cell ATAC-seq data, and shows it can identify cell types by analyzing open chromatin regions.

The accessible chromatin landscape of the hippocampus at single-cell resolution

The paper presents a single-cell chromatin accessibility map of the mouse hippocampus using sci-ATAC-seq, identifies cell-type-specific regulatory networks, and provides a resource for future studies.

High-throughput chromatin accessibility profiling at single-cell resolution

The paper develops a high-throughput single-cell ATAC-seq method and applies it to cluster PBMCs by hematopoietic cell type.

A cosine similarity-based method to infer variability of chromatin accessibility at the single-cell level

PRISM quantifies single-cell chromatin accessibility variation, outperforming existing methods by accounting for technical biases and revealing masked heterogeneity.

Cis-topic modelling of single cell epigenomes

The paper introduces cisTopic, a probabilistic framework for discovering cis-regulatory topics and cell states from single-cell epigenomics data, and validates its findings using RNA-seq co-expression networks and perturbation experiments.

Integrative analysis of single cell genomics data by coupled nonnegative matrix factorizations

The paper introduces coupled nonnegative matrix factorizations to integrate single cell RNA-seq and ATAC-seq data by coupling clustering across samples.

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

BROCKMAN identifies transcription factor activity variation in single-cell ATAC-seq data by analyzing k-mer frequencies associated with epigenomic marks.

Unsupervised clustering and epigenetic classification of single cells

This paper introduces scABC, an R package for unsupervised clustering of scATAC-seq data to classify cell types based on open chromatin regions.

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

This paper introduces scNMT-seq, a method for joint profiling of chromatin accessibility, DNA methylation, and transcription in single cells, and validates it in differentiating mouse embryonic stem cells.