scATAC-seq

Single nucleus analysis of the chromatin landscape in mouse forebrain development

The paper uses single nucleus ATAC-seq to analyze chromatin accessibility in mouse forebrain development, identifying cell-type-specific regulatory sequences and transcriptional regulators.

chromVAR: Inferring transcription factor variation from single-cell epigenomic data

chromVAR analyzes sparse scATAC-seq data to estimate motif-associated accessibility changes and cluster profiles while controlling technical biases.

Manifold Alignment Reveals Correspondence Between Single Cell Transcriptome and Epigenome Dynamics

The paper introduces MATCHER, a method that aligns single cell transcriptomic and epigenomic data to infer shared trajectories, revealing correlations between gene expression and epigenetic changes in mouse embryonic stem cells.

Dr.seq2: A Quality Control And Analysis Pipeline For Parallel Single Cell Transcriptome And Epigenome Data

Dr.seq2 is a QC and analysis pipeline for single cell transcriptome and epigenome data, providing reliable results on published datasets.

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

This paper introduces scNOMe-seq, a method to measure chromatin accessibility, DNA methylation, and nucleosome phasing in single cells, revealing CTCF footprints and nucleosome phasing distances.

Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation

The paper uses single-cell chromatin accessibility to map the continuous regulatory variation in human hematopoietic differentiation and identifies epigenomic heterogeneity within cell populations.