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Biostatistics & Epidemiology

  • Expression Predictor (ExP) ( a desktop application developed with Java™ programming language for classifying and predicting samples based on gene expression data using a simplified fuzzy adaptive resonance theory map (SFAM) neural network architecture.
  • Extracting Patterns and Identifying co-expressed Genes (EPIG) ( is a method for Extracting microarray gene expression Patterns and Identifying co-expressed Genes.
  • fdrMotif ( determines the number of binding sites in each sequence of a probability model by performing statistical tests.
  • GA/KNN ( selects the most discriminative variables for sample classification and may be used for analysis of microarray gene expression data, proteomic data or other high-dimensional data.
  • GADEM( is an unbiased de novo motif discovery tool implementing an expectation-maximization (EM) algorithm.
  • Genetic Algorithm Method for Optimizing a Position Weight Matrix ( implements a simple method to improve a poorly estimated position weight matrix using chromatin immunoprecipitation data.
  • Hybrid Design ( provides information for fitting log-linear models and carrying out statistical tests.
  • Modk-Prototypes ( clusters biological samples by simultaneously considering microarray gene expression data and classes of known phenotypic variables such as clinical chemistry evaluations and histopathologic observations.
  • mPopTag ( is a tool used to select or evaluate linkage disequilibrium tag SNPs for multiple populations.
  • ORIOGEN v 2.2 - Order Restricted Inference for Ordered Gene Expression ( analyzes gene expression data obtained from time-course/dose-response studies.
  • Phase-shifted Analysis of Gene Expression (PAGE) ( is an interactive tool that uses a line graph to dynamically illustrate the phase-shifted patterns of gene expressions based on the q-Cluster selected by the users.
  • SA-Modk-Prototypes ( for simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations using simulated annealing.
  • Systematic Variation Normalization (SVN) ( is a procedure for removing systematic variation in microarray gene expression data.
  • TAGster ( is a tool to select, evaluate and visualize LD tag SNPs for single or multiple populations.
  • TRIad Multi-Marker ( performs association tests for a child's or mother's genetic effects using multiple markers from triad families.

Physical & Analytical Chemistry

Structural Biology

  • NMR NOE Simulations ( calculates the time dependence of the diagonal and crosspeaks in a 2D NOESY experiment for a system undergoing chemical exchange using the full relaxation matrix.
  • NMR Scripts ( analyze multidimensional NMR data.
  • NvAssign ( software aids the process of protein resonance in NMR.

Molecular Biology

  • PCR Analyzer ( uses an algorithm that helps researchers examine polymerase chain reaction (PCR) data.

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Last Reviewed: October 07, 2008