# CellCraft: an extensible visual programming application for gene regulatory network inference

## TL;DR

CellCraft is a web-based tool that simplifies the analysis of gene regulatory networks from single-cell RNA sequencing data using an intuitive interface.

## Contribution

CellCraft introduces a visual programming interface and modular architecture for streamlined and extensible GRN inference.

## Key findings

- CellCraft integrates multiple GRN tools into a unified web application with a graphical user interface.
- The visual programming interface enhances accessibility and interpretation of complex GRN analyses.
- The modular design allows for easy incorporation of new single-cell analysis algorithms.

## Abstract

Reconstructing gene regulatory networks (GRNs) from single-cell RNA sequencing (scRNA-seq) data is fundamental for understanding cellular dynamics at the molecular level but requires sophisticated workflows. Here, we introduce CellCraft, a web-based application designed to streamline GRN inference. CellCraft integrates multiple GRN reconstruction tools, including TENET, within a unified web application featuring an intuitive graphical user interface. Notably, CellCraft provides a visual programming interface that simplifies the design and execution of complex multistep analyses, thereby enhancing accessibility and facilitating the visualization and interpretation of computational experiments. Furthermore, its modular plugin architecture ensures extensibility, enabling the incorporation of newly developed single-cell analysis algorithms. Consequently, CellCraft provides a user-friendly and extensible application for integrative GRN analysis of scRNA-seq datasets.

CellCraft is available on GitHub at https://github.com/cxinsys/cellcraft. The source code has been archived on Zenodo at 10.5281/zenodo.17865848.