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  • Gene expression - finding DE genes

    Hi

    I am working with Solexa RNAseq where I want to compare 2 classes (e.g. normal vs sick) with 3 biological samples in each (e.g. 3 patients) and find differentially expressed genes/tags between the 2 classes.

    Does anybody have suggestions on which test/program (preferable freeware) or online tool that I can use? Perhaps an R package?

    So far I have looked into SAGEBetaBin:

    and it seemed to be working fine a few months ago, but now I have troubles submitting.

    Thanks,
    Lene

  • #2
    hey,

    you might wqant to try the "edgeR" bioconductor package.

    The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.


    works well for me...

    cheers, florian

    Comment


    • #3
      Originally posted by florian View Post
      hey,

      you might wqant to try the "edgeR" bioconductor package.

      The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.


      works well for me...

      cheers, florian
      Thanks - I will look into that

      Comment

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