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    Robarts Research Institute

    Microarray Links


    Online Data Analysis Tools

    Sample Size Calculation NetAffx
    CyberT (Stat program)
    RINdb Venny 2.1
    Affy Regional Bias QC GenePattern
    Illumina Coverage Calculator Ribo-Zero rRNA Removal Kits Species Compatibility
    miR2Disease miRWalk 2.0

    Ontology and Pathway Analysis Tools

    Onto Express FatiGO
    Gostat GoToolBox
    Panther Ontologizer
    visANT DAVID
    BiNGO Enrichr
    Nexontology GeneMania
    String Reactome


    Academic Data Analysis Software

    Genotyping Console Agilent Technologies BioAnalyzer Expert Software (demo)
    Expression Console
    TIGR MultiExperiment Viewer The Comprehensive R Archive Network
    BioConductor R
    RMAExpress Microarray Sample Size Determination
    Hierarchical Clustering Explorer CRLMM (SNP genotyping algorithm)
    Chipster The Bio-Array Resource for Arabidopsis Functional Genomics
    iArray Analyzer CNAG
    Expander GSEA
    SAM DAVID (biological interpretation)
    BRB ArrayTools
    ATHENA MAT (Model based Analysis of Tiling arrays)
    Data Assist (for TaqMan RT-PCR data) Affymetrix Integrated Genome Browser (IGB)
    Q-value BiNGO
    CisGenome TileMapper
    TAS MatchMiner
    ComBat TAC

    Pathway Resources

    Pathway Express GeneAssist Pathway Atlas
    Sigma-Aldrich Search Your Favorite Gene


    Network Tools

    Ingenuity Pathway Analysis


    London Regional Core Facilities

    London Regional Proteomics Centre Translational Research Centre
    London Regional Transgenic and Gene Targeting Facility  


    List Servers

    SEQAnswers BioConductor
    qPCR Forum  


    Commercial Data Analysis Software

    Partek Genomics Suite CLCBio Genomics Workbench


    Selected Reading

    GenomeWeb Tech Guides

    Barr, Gordon A., Gao, Puhong. 2005. Issues for Consideration in the Analysis of Microarray Data in Behavioural Studies. Addition Biology 10,15-21 (March 2005).

    Affymetrix. 2004. Sample Pooling for Microarray Analysis: A Statistical Assessment of Risks and Biases. Affymetrix.

    Affymetrix. 2003. GeneChip Expression Analysis: Experimental Design, Statistical Analysis and Biological Interpretation. Affymetrix.

    Affymetrix. 2003. Data Analysis Fundamentals Manual. Affymetrix.

    Affymetrix. 2002. Statistical Algorithms Description Document Affymetrix.

    Causton, C. Helen, Quackenbush, J. and Brazma A. 2003. Microarray Gene Expression Data Analysis: A Beginner's Guide. Blackwell Publishing.

    Dudoit, S., Gentleman, R.C., and Quackenbush, J. 2003. Open Source Software for the Analysis of Microarray Data. BioTechniques 34:S45-S51 (March 2003).

    Knudsen, S., 2002. A Biologist's Guide To Analysis of DNA Microarray Data. John Wiley & Sons, Inc.

    Microarray Expression Data Analysis References

    Yee Hwa Yang and Terry Speed. 2002. Design Issues For cDNA Microarray Experiments. Nature Reviews: Genetics. 2002 Aug;

    Priti Hegde, Rong Qi, Kristie Abernathy, Cheryl Gay, Sonia Dharap, Renee Gaspard, Julie Earle-Hughes, Erik Snesrud, Norman Lee, and John Quackenbush. 2000. A Concise Guide to cDNA Microarray Analysis. Biotechniques 29(3):548-50,552-4 (Sep. 2000) passim. Review.

    Affymetrix Library Files


    Equipment & Reagent Suppliers

    Affymetrix Agilent 2100 Bioanalyzer
    Ambion RNA 6000 Ladder Genisphere
    Qiagen RNeasy kit


    Next-Generation Sequencing Resources

    Alignment algorithms Alignment Visualization software
    SeqAnswers SeqAnswers software list
    SFF Tools FastQC
    Galaxy IGV
    BioEdit NextGENe
    Mothur (Microbial ecology) Aligner Comparison
    Genome Analysis Tool Kit Savant Genome Browser
    RNA-Seq Design Calculator R Power Analysis


    qPCR Resources

    New to Real-Time PCR? Start here! Tools
    Tutorials & Guides Troubleshooting
    qPCR Handbook


    Robart's Research Institute

    University of Western Ontario

    Site designed by Ericka Simon

    Maintained by David Carter

    Last update: Wednesday, May 9, 2018