Software Resources

  • Gene Expression Miner

    This Strain Survey GEM holds data for a gene expression survey of 26 inbred mouse strains. Users can perform simple or advanced queries to find various locations of interest.

  • Genome Navigator

    Online tool used to find genes and transcripts in designated regions. Users can either enter a range manually or click and drag to select a region of interest.

  • Marker regression programs

    These programs are based on marker regression and are designed for detecting covariate effects and interactions from inbred line cross data.

  • HMM

    This software is used to fit Hidden Markov Models in Stochastic models for heterogeneous DNA sequences.

  • J/maanova

    J/maanova is an open sourced desktop application developed with the aim of simplifying the analysis of microarray experiments.

  • J/qtl

    J/qtl is a Java graphical user interface (GUI) for the popular QTL data analysis software R/qtl.

  • JAX Colony Management System

    The JAX Colony Management System (JCMS) is a free and supported multi-user relational database system for managing research mouse colonies.

  • Mouse Phylogeny Viewer

    Custom genome browser provides detailed answers to questions on the haplotype diversity and phylogenetic origin of the genetic variation underlying any genomic region of most laboratory strains.

  • Pseudomarker programs

    Pseudomarker is a set of programs written in MATLAB for the analysis of QTL data from inbred line crosses.

  • PubArray

    PubArray is a desktop application that allows you to turn the analyzed results of your microarray experiment into a web application which is accessible via your browser.

  • R/maanova

    R/maanova is an extensible, interactive environment for Microarray analysis.

  • R/qtl

    R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.

  • MAANOVA 2.0

    MAANOVA is a set of functions written in Matlab for the analysis of variance on microarray data.

  • MoDIS - Mouse Disease Information System

    MoDIS links to the Pathbase.net website to provide detailed information and annotated images of similar lesions in laboratory mice, making it a unique and useful training aid.