Software
- NetImpute: a network-based scRNA-seq data imputation tool (Zand and Ruan, 2020).
- Arabidopsis Co-expression Network-based Resource: Web-based tool to explore Arabidopsis gene co-expression network and modules, enriched functional modules, cis-regulatory elements for modules and individual genes.
- LOGO2PWM: a tool to convert sequence logo to position weight matrix (Gao et. al. 2017).
- Network-based differential analysis of Chromatin interactions: Software and data for our JBCB paper (Liu & Ruan 2017).
- Network-based pathway enrichment analysis : Software and data for our Genes paper (Liu et. al. 2017).
- Multiple instance learning for Protein-DNA interaction modeling: Supplemental data and software for our bioinformatic paper (Gao & Ruan 2017).
- Personalized Committee Classifier: Supplemental data and software for our bioinformatic paper (Jamiul et al. 2014).
- Random Walk with Resistance : Supplemental data and software for our bioinformatic paper (Lei & Ruan 2013).
- CommFinder: A Cytoscape plugin for finding community structures
- Qcut and HQcut (for finding communities in networks). Also includes some scripts for visualizing clustering results, and for constructing and clustering gene co-expression networks. Download
- BDTree (a Bi-dimensional Regression Tree approach for modeling transcriptional regulation). Download
- Iterative Loop Matching (for predicting RNA secondary structures with pseudoknots), web server | Download