Software
cfSNV
cfSNV is an ultra-sensitive somatic SNV caller for cfDNA sequencing, using advanced models for mutation profiling and error suppression. Available as an R package and Docker image on GitHub.
CancerDetector
CancerDetector detects trace amounts of tumor-derived cfDNA in plasma by modeling methylation patterns of CpG sites, enabling ultrasensitive identification at the read level.
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CancerLocator
CancerLocator is a Java tool for non-invasive cancer diagnosis using cell-free DNA methylation. It identifies tumor presence, location, and tissue origin. Available on GitHub and Zenodo.
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Struct2fun
Struct2fun identifies 3D chromatin clusters from Hi-C data, highlighting frequent structures across genome populations and single-cell data.
TopDom
TopDom is an efficient tool for identifying topological domains with statistical quality evaluation. It uses a single parameter, window size, with optimization guidelines. Available on Zhoulab GitHub.
Hi-Corrector
Hi-Corrector removes biases from chromatin contact matrices. It's fast, scalable, memory-efficient, and implemented in ANSI C. Available on Zhoulab GitHub.
DiseaseConnect Server
DiseaseConnect is a public web server for analyzing disease connectivity using omics data, GWAS, gene expression, and literature. It also includes drug-disease relationships and clinical co-morbidity data.
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Integrative Array Analyzer
iArray is a software platform for integrating and visualizing multiple microarray datasets, improving signal-to-noise ratio and biological inference.
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CODENSE
CODENSE mines coherent dense subgraphs from multiple biological networks efficiently by simplifying the problem into two special graphs.
MODES
MODES (Mining Overlapping DENSE Subgraphs) efficiently identifies dense and overlapping subgraphs, and is used in CODENSE for subgraph analysis.
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