DIRECT-NET: Inferring CREs and constructing regulatory networks from single cell multi-omics data

Capabilities

DIRECT-NET is an R toolkit for inferring CREs and constructing regulatory networks from parallel single cell RNA-seq and ATAC-seq data or only single cell ATAC-seq data.

Installation

To make it easy to run DIRECT-NET in most common scRNA-seq and scATAC-seq data analysis pipelines, DIRECT-NET is now implemented within Seurat V4/Signac workflow. Please first install Seurat R pacakge (>= 4.0) via install.packages('Seurat').

DIRECT-NET R package can then be easily installed from Github using devtools:

devtools::install_github("zhanglhbioinfor/DIRECT-NET")

Installation of other dependencies

• Install Signac pacakge : devtools::install_github("timoast/signac", ref = "develop"). Please check here if you encounter any issue.
• Install Cicero package: devtools::install_github("cole-trapnell-lab/cicero-release", ref = "monocle3"). Please check here if you encounter any issue.

Tutorials

The implementent of DIRECT-NET is now seamlessly compatible with the workflow of Seurat V4 package.

Examples

• Demo of DIRECT-NET on parallel scRNA-seq and scATAC-seq data of PBMC

• Demo of DIRECT-NET on parallel scRNA-seq and scATAC-seq data of A549

• Demo of DIRECT-NET on scATAC-seq data of GM12878

• Demo of DIRECT-NET on scATAC-seq data of human Brain

Help

If you have any problems, comments or suggestions, please contact us at Lihua Zhang (zhanglh@whu.edu.cn).