Supported and Installed Software


  • GenoPub DAS2 (Distributed Annotation System) server
  • HCI Supplemental Paper Info Repository
  • GNomEx - NextGen and Microarray LIMS and Analysis database

Next-Generation Sequencing

  • Sequencing with Illumina sequencers, recommendations
  • USeq - Project analysis software for chIP-seq, RNA-seq, bis-seq, and more
  • Partek genomics suite
  • Tomato - Framework for pipelines to analyze sequencing data in high performance clusters
  • Solexa Pipeline - Outline of requirements for supporting an Illumina sequencer

Genome Browsers

  • IGB - Highly sophisticated, cross-platform, stand-alone genome browser designed for real-time visualization and manipulation of large genomic datasets
  • UCSC GB - Well-supported web genome browser centered on complex organisms

Gene Expression

  • Partek genomics suite
  • Bioconductor - Microarray analysis software library written in R, contributed by a variety of labs Includes Rank Product (RankProd) analysis, Affymetrix (Affy) normalization package
  • R - Statistics programming language needed for Bioconductor
  • GeneSifter - Web-based commercial analysis tool with clustering, KEGG pathway, and gene ontology analysis methods
  • Spotfire DecisionSite - (Windows only) Commercial data visualization and analysis tool well suited to microarray data analysis, with optional functional genomics and statistics features useful for microarray data normalization and analysis
  • MeV from TM4 - Public domain analysis program with a wide variety of analysis tools including clustering, classification, and statistical analysis methods. Runs under MacOS, Windows, and Linux operating systems. Can be used for analysis of expression data from Agilent, Affymetrix, and spotted cDNA arrays.
  • SAM - (Significance Analysis of Microarrays) Statistical method for microarray data analysis. Stanford University distributes a Microsoft Excel add-in that performs SAM within an Excel spreadsheet. An excellent implementation of SAM is also available within MeV.
  • PAM - (Prediction Analysis for Microarrays) Sample classification method which uses the nearest shrunken centroid method. PAM builds a classifier based on a training data set, which can then classify unknown samples. Implemented in R.



  • AgilentFilter - tool for filtering and reformatting Agilent microarray data files
  • CreateAnalysis - java app for creating a new analysis entry in GNomEx to deposit analysis files in a batch job

Contact Us

Genomics Director
Brian K. Dalley, PhD

Bioinformatic Analysis Director
David Nix, PhD


HCI Senior Director Oversight
Bradley Cairns, PhD

Faculty Advisory Committee Chair
Bradley Cairns, PhD

Faculty Advisory Committee Members
Richard Clark, PhD
Jason Gertz, PhD
Christopher Gregg, PhD
Philip Moos, PhD
Sean Tavtigian, PhD
Katherine Varley, PhD
Joseph Yost, PhD