dbscATAC is a specialized database offering comprehensive annotations of 213,835 super-enhancers across 520 tissue/cell types from 3 species, as well as 347,484 gene markers, 13,470,526 enhancers, and 10,402,346 enhancer-gene interactions, and 43,202,785 TF binding sites derived from 1,668,076 single cells of scATAC-seq data spanning 1,028 tissue/cell types in 13 species. The predicted results are available in an interactive website http://singlecelldb.com/dbscATAC/index.php.

Overview of dbscATAC

Dependencies

To conduct prediction of super-enhancers, typical enhancers, and gene markers, following softwares are required:
✯ ROSE
✯ R version > 4.2
✯ Signac 1.12.0
✯ Seurat 5.1.0
✯ cicero 1.3.9
✯ Perl >5.16.3
✯ bedtools > 2
✯ macs2 2.2.6
✯ sinto 0.10.1
✯ deeptools > 2
✯ python3

Tutorial

Prediction-of-superenhancers : Predict single-cell superenhancers using the GSE111586 dataset for human
Prediction-of-enhancers : Predict single-cell enhancers by the GSE149683 dataset for mouse
Identification-of-markers : Identify single-cell gene markers using the GSE163697 dataset for fly

Download of results

All the single-cell chromatin accessibility annotation data are available at:
http://singlecelldb.com/dbscATAC/download.php