BIRD: Big data Regression for predicting DNase I hypersensitivity

Overview: BIRD is a software to predict DNase I hypersensitivity (DNase-seq signal) based on gene expression data (support both human exon array and RNA-seq data). Using a pre-built model and input gene expression data, BIRD is capable to predict DNase-seq signal genome-wide (~1M genomic loci). BIRD provided two types of outputs: (1) data matrix format or (2) WIG format. Users can easily visualize the predicted DNase-seq signals in UCSC genome browser.

BIRD is available here.

PDDB: Predicted DNase I hypersensitivity database

Overview: PDDB is a database of DNase I hypersensitivity profiles for thousands of biological samples predicted based on gene expression.

PDDB is available here.

SCRAT: a toolbox for analyzing single-cell regulome data

Overview: SCRAT is a Single-Cell Regulome Analysis Toolbox with a graphical user interface, for studying cell heterogeneity using single-cell regulome data.

SCRAT is available here.