Oklahoma State University
Software Analysis Tools | Print |  E-mail

Categorized software tools: (incomplete list)

Array Design |   Image Analysis |   Ratio Analysis |   Clustering |   Oligo-Design |   Align/Assemble  |   Miscellaneous

For array design, fabrication and maintaining a database of clones and arrays

  • Longhorn Array Database (LAD): A Stanford Microarray Database powered microarray data warehouse
  • BASE:A web-based microarray database system
  • OmniGrid Gridder: Microarray design and fabrication software for the OmniGrid 100. This software also assists in coordination of spots-to-probes
  • CloneTracker CE: CloneTracker CE data management software is available to assist researchers in the design and fabrication of high-density microarrays by assisting in automated generation of AxSys-specific printing scripts and maintaining the coordination of spots-to-libraries
  • TIGR Madam:  Microarray Data Manager  (http://www.tm4.org/madam.html)


For image analysis and spot quantification:

  • GenePix Pro: This software package is designed for array image analysis and quantification and provides highly desired processing features such as auto-adjustment of spots within grids, alignment of non-overlayed images, import of clone layout within the array in addition to extraction and quantification of gene expression data and can import third-party images generated from microarrays or macroarrays
  • ScanArray: The ScanArray software is used to control the ScanArray Express (PerkinElmer) confocal laser scanning device. This software generates tiff images for further analysis and quantification
  • ImaGene 4.2: For the extraction and quantification of gene expression data generated by most third-party array scanners. Feartures include the ablity to simultaneously load and analyse up to five images, automated spot finding, segmentation and analysis tools. Additionally, GeneSight-Lite comes bundled with ImaGene
  • ScanAlyze: Processes TIFF images of microarrays with pixel and spot analyses and outputs as tab-delimited text files for transfer to any database.