Yaohua Hu - Software

Matlab

• LpRGNI (Lp Regularization for Gene Network Inference)
  - A Matlab tool for predicting gene regulatory network by using the LASSO-type estimators, including the L0, L1 and L(1/2) regularization models, and from both high-throughput gene expression data and transcription factor.
  - Reference:
  

  • J. Qin, Y. Hu, F. Xu, H. K. Yalamanchili and J. Wang, Inferring gene regulatory networks by integrating ChIP-seq/chip and transcriptome data via LASSO-type regularization methods, Methods, 67: 294-303, 2014. [link]

• GSO (Group Sprase Optimization for Cell Fate Conversion Prediction)
  - A Matlab tool for predicting master transcription factors (TFs) for cell fate conversion by using the L(2,0) group sparse optimization method, and from eithor single-cell or bulk OMICs data. [GitHub]
  - Reference:
  

  • J. Qin*, Y. Hu, J.-C. Yao, R. W. T. Leung, Y. Zhou, Y. Qin and J. Wang, Cell fate conversion prediction by group sparse optimization method utilizing single-cell and bulk OMICs data, accepted in Briefings in Bioinformatics, 2021. [link]

R

• GSparO (Group Sparse Optimization)
  - An R pacakage for solving the L(p,q) regularization of group sparse optimization problem by implementing the proximal gradient algorithm.
  - Reference:
  

  • Y. Hu, C. Li, K. Meng, J. Qin and X. Yang, Group sparse optimization via L(p,q) regularization, Journal of Machine Learning Research, 18(30): 1-52, 2017. [link]

• GSO (Group Sprase Optimization for Cell Fate Conversion Prediction)
  - An R pacakage for predicting master transcription factors (TFs) for cell fate conversion by using the L(2,0) group sparse optimization method, and from eithor single-cell or bulk OMICs data. [GitHub]
  - Reference:
  

  • J. Qin*, Y. Hu, J.-C. Yao, R. W. T. Leung, Y. Zhou, Y. Qin and J. Wang, Cell fate conversion prediction by group sparse optimization method utilizing single-cell and bulk OMICs data, accepted in Briefings in Bioinformatics, 2021. [link]

Webserver

• CrusTF (Crustacean Transcription Factors)
  - A comprehensive resource for evolutionary and functional studies of crustacean transcription factors.
  - Reference:
  

  • J. Qin, Y. Hu, K. Ma, X. Jiang, C. Ho, L. Tsang, L. Yi and K. Chu, CrusTF: A comprehensive resource for evolutionary and functional studies of crustacean transcription factors, BMC Genomics, 18(1): 908, 2017. [link]

• CORN (Condition Orientated Regulatory Networks)
  - A library of 1805 different types of specific conditions (small molecule/drug treatments and gene knockdowns) to 9554 transcriptional regulatory networks (TRNs) in 25 human cell lines involving 204 transcription factors (TFs) that comes with an online TRN matching tool.
  - Reference:
  

  • R. W. T. Leung#, X. Jiang#, X. Zong#, Y. Zhang, X. Hu, Y. Hu* and J. Qin*, CORN - Condition Orientated Regulatory Networks: bridging conditions to gene networks, Briefings in Bioinformatics, 23(6): bbac402, 2022. [link]