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  • ChIP Seq data analysis

    Hi all
    I am just wondering that if anyone knows any statistical analysis tools for comparing output from different ChIP Seq data analysis tools. It could also be useful any recommendations for comparison.
    Any suggestions would be gratefully appreciated
    Thanks in advance

  • #2
    What do you want to compare? Most software output a list of peaks. YOu want to know which peak lists give better ranks? Without gold standard it'll be difficult.

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    • #3
      I have developed R scripts for multiway analysis of multifactor ChIP-seq coverage profiles and invite collaboration to incorporate the scripts into a BioConductor package.
      Interested?

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      • #4
        Originally posted by Karl Kornacker View Post
        I have developed R scripts for multiway analysis of multifactor ChIP-seq coverage profiles and invite collaboration to incorporate the scripts into a BioConductor package.
        Interested?
        Hi Karl,
        Thanks for your help... I would be really grateful if you could share me the scripts.
        Kind regards

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        • #5
          I am preparing a publication on previously unrecognized biologically significant enrichment patterns found by application of a novel multiway data analysis method to a superset of publicly available ChIP-seq datasets. I am inviting pre-publication collaboration, with possible co-authorship.

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          • #6
            Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, et al. (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9(11): e1003326. doi:10.1371/journal.pcbi.1003326

            http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003326
            Pedro Madrigal

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