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Software

Supported and Installed Software:

Contents

Repositories

  • The Core's GenoPub DAS2 (Distributed Annotation System) server
  • The HCI's Supplemental Paper Info Repository
  • GNomEx - the cores NextGen and Microarray LIMS and Analysis database.

Next Generation Sequencing

  • Sequencing with our Illumina sequencers, recommendations
  • USeq project analysis software, developed by the core for chIP-seq, RNA-seq, bis-seq, etc.
  • Partek genomics suite is now available on a desktop Macintosh in the Bioinformatics Shared Resource. You can reserve time on this machine using the University Cores Scheduling web site.
  • Tomato - a framework for pipelines to analyze sequencing data in high performance clusters
  • Solexa Pipeline - outline of requirements for supporting an Illumina sequencer

Genome Browsers

  • IGB - a highly sophisticated, cross platform, stand alone genome browser designed for real time visualization and manipulation of large genomic datasets. IGB has been adopted by the Core for genomic analysis.
  • UCSC GB - a well supported web genome browser, complex organism centric

Gene Expression

  • Partek genomics suite is now available on a desktop Macintosh in the Bioinformatics Shared Resource. You can reserve time on this machine using the University Cores Scheduling web site.
  • 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. Combines statistical analysis tools with clustering, KEGG pathway, and Gene Ontology analysis methods. Contact the Microarray Bioinformatics Core for access.
  • Spotfire DecisionSite - a commercial data visualization and analysis tool that is well suited to microarray data analysis. It has optional Functional Genomics and Statistics features that are useful for microarray data normalization and analysis. Spotfire is available on the Windows platform only.
  • MeV from TM4 - a public domain analysis program that combines a wide variety of analysis tools including clustering, classification, and statistical analysis methods. It runs under MacOS, Windows, and Linux operating systems, and can be used for analysis of expression data from Agilent, Affymetrix, and spotted cDNA arrays.
  • SAM - (Significance Analysis of Microarrays) is a 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) is a 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.

Tiling

Utilities

  • 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.