This repository contains plugin configurations and information for CellCraft, a web-based visual programming application for gene regulatory network (GRN) inference.
CellCraft integrates multiple GRN reconstruction tools through its modular plugin system. This repository serves as a central hub for managing and documenting all available plugins that can be used within the CellCraft environment.
| Plugin | Description | Paper | GitHub |
|---|---|---|---|
| TENET | Transfer Entropy-based Network Reconstruction - Employs transfer entropy from information theory to infer causal relationships in gene regulatory networks from single-cell RNA-seq data | Kim et al., NAR 2021 | neocaleb/TENET |
| FastTENET | Accelerated TENET Implementation - An optimized version of TENET that leverages manycore computing for faster GRN inference while maintaining accuracy | Sung et al., Bioinformatics 2024 | cxinsys/fasttenet |
| SCODE | Efficient Regulatory Network Inference During Differentiation - Infers regulatory networks from single-cell RNA-seq data during cell differentiation using ordinary differential equations | Matsumoto et al., Bioinformatics 2017 | hmatsu1226/SCODE |
| SCRIBE | Causal Network Inference Using Single-Cell Expression Dynamics - Uses restricted directed information to infer causal regulatory networks from coupled single-cell expression dynamics | Qiu et al., Cell Systems 2020 | cole-trapnell-lab/Scribe |
| LEAP | Pseudotime-based Co-expression Network Construction - Constructs gene co-expression networks for single-cell RNA-seq data using pseudotime ordering | Specht & Li, Bioinformatics 2016 | cran/LEAP |
| GRNBOOST2 | Scalable Gene Regulatory Network Inference - Provides efficient and scalable inference of gene regulatory networks using gradient boosting | Moerman et al., Bioinformatics 2018 | aertslab/GRNBoost |
| GENIE3 | Tree-based Network Inference - Infers regulatory networks from expression data using tree-based methods (Random Forests or Extra-Trees) | Huynh-Thu et al., PLOS ONE 2010 | vahuynh/GENIE3 |
If you would like to contribute a new plugin or improve existing ones, please:
- Fork this repository
- Create a feature branch
- Submit a pull request with a clear description of your changes