scATAC-seq

simATAC: A single-cell ATAC-seq simulation framework

simATAC generates synthetic scATAC-seq datasets with known cell labels to benchmark analytical pipelines.

Fast searches of large collections of single cell data using scfind

scfind enables efficient querying of single-cell data to evaluate marker genes, perform in silico gating, and support multi-omics analyses.

SnapATAC: A Comprehensive Analysis Package for Single Cell ATAC-seq

SnapATAC is a software package for analyzing scATAC-seq data, revealing regulatory elements and transcriptional regulators in mouse brain cells.

ArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis

ArchR, an HDF5-backed R suite for end-to-end scATAC-seq analysis, outpaces SnapATAC and Signac and processes over 1.2 million simulated cells within 8 h on a laptop.

Spatially-mapped single-cell chromatin accessibility

The paper introduces sciMAP-ATAC, a method for spatially resolved single-cell chromatin accessibility profiling, and applies it to study cortical lamination, spatial trajectories, and ischemic infarct progression in mouse and human tissues.

Single-cell ATAC and RNA sequencing reveal pre-existing and persistent subpopulations of cells associated with relapse of prostate cancer

The paper uses single-cell ATAC and RNA sequencing to identify pre-existing and treatment-persistent stem-like cell subpopulations in prostate cancer models that predict treatment response.

SCAN-ATAC Sim: a scalable and efficient method for simulating single-cell ATAC-seq from bulk-tissue experiments

SCAN-ATAC-Sim simulates scATAC-seq data from bulk ATAC-seq to benchmark analysis methods with known cell-type labels.

BBrowser: Making single-cell data easily accessible

A downloadable application pairs a curated single-cell database with a big-data analytics layer and a visualisation module for exploring single-cell omics data.

Unbiased integration of single cell multi-omics data

bindSC integrates single-cell multi-omics data accurately by aligning rows and columns without approximations, outperforming existing methods in various biological contexts.

Single-cell multi-omics reveals elevated plasticity and stem-cell-like blasts relevant to the poor prognosis of KMT2A-rearranged leukemia

This study uses single-cell multi-omics to identify lineage plasticity and stem-cell-like blasts in KMT2A-rearranged leukemia, linking these features to poor prognosis in infants.

Mapping genetic effects on cell type-specific chromatin accessibility and annotating complex trait variants using single nucleus ATAC-seq

The paper uses snATAC-seq to map chromatin accessibility QTLs in immune cell types and fine-maps complex trait loci, identifying cell type-specific causal variants.

FITs: Forest of imputation trees for recovering true signals in single-cell open chromatin profiles

FITs recovers true signals from sparse and noisy single-cell open-chromatin profiles by using a forest of imputation trees to avoid bias and preserve cell-type-specific activity.

ChromSCape : an R/Shiny application for interactive analysis of single-cell chromatin profiles

ChromSCape is an R/Shiny tool for analyzing single-cell chromatin data, enabling subpopulation identification and differential region analysis in epigenomic studies.

MarkovHC: Markov hierarchical clustering for the topological structure of high-dimensional single-cell omics data

MarkovHC is a clustering algorithm that identifies cell types, trajectories, and critical points in single-cell omics data by reconstructing a pseudo-energy landscape based on metastability theory.

Coupled Co-clustering-based Unsupervised Transfer Learning for the Integrative Analysis of Single-Cell Genomic Data

This paper introduces a coupled co-clustering-based transfer learning method for integrating multimodal single-cell genomic data, improving clustering performance and matching cell subpopulations across data types.

Single-cell epigenomic identification of inherited risk loci in Alzheimer's and Parkinson's disease

The paper uses single-cell epigenomic data to identify functional SNPs associated with Alzheimer's and Parkinson's disease, revealing novel gene-disease associations and regulatory mechanisms.

scATAC-Seq reveals epigenetic heterogeneity associated with an EMT-like process in male germline stem cells and its regulation by G9a

The paper uses scATAC-seq to identify epigenetic heterogeneity in male germline stem cells associated with an EMT-like process and shows G9a regulates this process.

Jointly Defining Cell Types from Multiple Single-Cell Datasets Using LIGER

The paper provides a protocol for using LIGER to jointly define cell types from multiple single-cell datasets, including RNA-seq and ATAC-seq data.

Single-cell multimodal profiling of proteins and chromatin accessibility using PHAGE-ATAC

The paper introduces PHAGE-ATAC, a method for simultaneous single-cell measurement of surface proteins, chromatin accessibility, and mtDNA-based clonal tracing, and demonstrates its application in human immune cells.

Unsupervised manifold alignment for single-cell multi-omics data

This paper applies and extends MMD-MA to align single-cell transcriptome and chromatin accessibility data from ~2000 cells, demonstrating its scalability and accuracy.

Evolution of the Analytical Scattering Model of Live Escherichia Coli

The paper revises a scattering model for live E. coli to better fit experimental data and reveals structural differences between strains.

Diversification of Reprogramming Trajectories Revealed by Parallel Single-cell Transcriptome and Chromatin Accessibility Sequencing

This study uses scRNA-Seq and scATAC-Seq to show that human reprogramming occurs through asynchronous, diverse trajectories with distinct regulatory networks.

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

This paper introduces ASAP-seq, a method to simultaneously profile chromatin accessibility, protein levels, and mtDNA in single cells, demonstrating its application in hematopoietic differentiation and T cell perturbations.

TEA-seq: a trimodal assay for integrated single cell measurement of transcription, epitopes, and chromatin accessibility

The paper introduces TEA-seq, a trimodal assay that integrates scRNA-seq, cell surface epitopes, and scATAC-seq to improve single-cell analysis of transcription, epitopes, and chromatin accessibility.

Single-cell analysis of chromatin silencing programs in developmental and tumor progression

This paper develops scCUT&Tag to profile H3K27me3 in single cells, distinguishing cell types in blood and identifying PcG activity changes in brain tumors before and after treatment.

Simultaneous deep generative modeling and clustering of single cell genomic data

scDEC uses deep generative networks to simultaneously model and cluster scATAC-seq data, showing better performance than existing tools and enabling trajectory inference and cell type discovery.

Cytokine priming of naive CD8+ T lymphocytes modulates chromatin accessibility that partially overlaps with changes induced by antigen simulation

This study shows cytokine priming of naive CD8+ T cells changes chromatin accessibility, with some overlaps seen with antigen stimulation, suggesting a poised state for enhanced TCR responsiveness.

Multiomics analysis reveals extensive epigenome remodeling during cortical development

The paper uses multiomics data to map regulatory changes in the mouse neocortex during development, identifying novel enhancer-gene pairs and epigenetic remodeling patterns.

The impact of chromatin remodeling on gene expression at the single cell level in Arabidopsis thaliana

The paper uses sNucRNA-seq and sNucATAC-seq to study chromatin remodeling's impact on gene expression in Arabidopsis root nuclei, revealing cell-type-specific chromatin accessibility patterns.

A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis

This study identifies a primed chromatin state in oligodendroglia that facilitates rapid activation of immune gene programs in multiple sclerosis.