BBTD

Data and code for the paper: Reconstruction of gene regulatory networks for Caenorhabditis elegans using tree-shaped gene expression data.

Data

All real and processed datasets involved in the paper can be downloaded from Zenodo. Please download all the .rar files and decompress them. Place the decompressed folders and the .csv file in the data folder (Researchers should create it at the root path by themselves).

Tutorial

• Check and Install Required R Packages: Before running the tutorial, it is recommended to check and install all the required R packages. Please see requirements.txt for the list of dependencies.

• Run the Tutorial: After preparing the R environment, researchers can follow the tutorial to reproduce data integration and BBTD on real datasets. Refer to Tutorial.Rmd for detailed instructions. Since processing the raw data can be time-consuming, we recommend directly applying the BBTD method to the processed data available in the readydata directory.

License

BBTD is licensed under the GNU General Public License v3.0.

Reference

Wu Y, Zhou D, Hu J. Reconstruction of gene regulatory networks for Caenorhabditis elegans using tree-shaped gene expression data[J]. Briefings in Bioinformatics, 2024, 25(5).

Contact

For any questions about BBTD, please contact the corresponding author, Prof. Jie Hu via email at hujiechelsea@xmu.edu.cn.