Supported and Installed Software


  • 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
  • Solexa Pipeline - Outline of requirements for supporting an Illumina sequencer

Genome Browsers

  • 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.


  • Agilent ChIP Analytics - for ChIP-chip experiments
  • Agilent CGH Analytics - Variety of quality control and aberration detection analyses on CGH arrays
  • MeV from TM4 can perform some CGH analyses, as well as gene expression analysis.

Contact Us

Genomics Director
Brian K. Dalley, PhD

Bioinformatic Analysis Director
David Nix, PhD

Bioinformatic Analysis Associate Director
Timothy Parnell, 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