Software





KEGG2Net identifies gene-gene interaction networks from KEGG pathways and further constructs directed acyclic graphs (DAGs) from these networks for approaches like Bayesian Networks. KEGG2Net provides several alternative methods for cycle removal. Citation



FQStat performs quality control (QC) analysis for DNA/RNA sequencing fastq files using a parallel programming architecture. FQStat automatically configurates system parameters for optimum performance and flags low-quality samples. Citation




dbCGI is a web application that consists of a database and a suite of tools for analyzing and annotating CpG islands (CGIs).Citation




BNP (Bayesian Network Prior) provides a means to use external knowledge in building gene interaction networks using high-throughput biological data. BNP itself is a Bayesian Network that depicts the dependency structure between evidence types that imply an interaction event between two genes. Citation




BPA (Bayesian Pathway Analysis) transcends popular enrichment analysis methods by considering the topology of a pathway when determining its association with given high-throughput biological data. Citation1 Citation2




OS Distance calculates the Otu-Sayood distance measure for a set of sequences. OS distance is an alignment-free approach that is based on an information-theoretic method to generate sequences. Citation




MineData (Coming soon) is a MATLAB-based user-friendly tool with enhanced GUI capabilities that provides mining multi-dimensional datasets using statistical, mathematical, and computational methods performing tasks like filtering, correlation, clustering, and classification analysis




ASSESS (Assigning Significance to Subclusters of Experimental SampleS) is a stand-alone computer program to assign statistical significance to clustering of multi-dimensional data. Citation




STAGE (Statistical Analysis of Gene Expression) is a stand-alone computer program to analyze gene microarray data. STAGE is discontinued and replaced by MineData. Citation




DAC-FS (A Divide And Conquer Approach to Fragment Assembly) is a computer program that calculates the contigs resulting from a shotgun sequencing data. DAC-FS simultaneously solves the overlap, layout, and consensus phases by iteratively clustering the fragments (or consensus sequences) with respect to their average mutual information (AMI) profiles and processing each cluster separately. Citation

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