Software & Tools

SCATE

Single-Cell ATAC-seq signal Extraction and Enhancement

Extracts and enhances signal from sparse single-cell ATAC-seq data by leveraging information across cells and genomic loci. Enables accurate characterization of regulatory activity and cell-type heterogeneity.

BIRD

Big Data Regression for DNase I Hypersensitivity

Predicts genome-wide chromatin accessibility (DNase-seq signal) from gene expression data. Generates predictions across ~1 million genomic loci using a pre-built regression model.

SCRAT

Single-Cell Regulome Analysis Toolbox

An interactive Shiny toolbox for analyzing single-cell regulome data (scATAC-seq, scChIP-seq). Provides clustering, visualization, and regulatory feature analysis with no coding required.

FUNCODE

Functional Conservation of Regulatory Elements

Quantifies functional conservation of human and mouse regulatory elements, enabling comparative analysis of cis-regulatory activity across species.

Hi-Plex CUT&Tag

Combinatorial Chromatin Regulatory Mapping

A high-throughput multiplexed CUT&Tag approach for simultaneous profiling of multiple chromatin regulatory factors, enabling global mapping of combinatorial epigenetic states.

scMBERT

Single-Cell Multiomic Representation Learning

A pre-trained BERT-based deep learning model for single-cell multiomic data representation and prediction, enabling cross-modal inference and cell-type annotation.