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bioanalyzeR: New R package for data from the Agilent Bioanalyzer and TapeStation

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  • bioanalyzeR: New R package for data from the Agilent Bioanalyzer and TapeStation

    I wrote an R package for importing electrophoresis data from the Agilent Bioanalyzer and TapeStation and graphing the results with ggplot2 or analyzing them in more depth:

    package on GitHub
    vignette

    One particular application is for sequencing library QC, where the variable of interest is the size distribution of your sample by molarity, but the Agilent software only shows you total fluorescence, which is proportional to mass instead of molarity and therefore gives you a misleading representation.

    For example, here's the same library shown with fluorescence vs. log-scaled molecule length (analogous to the Agilent software's display) and then with molarity/bp vs. linear-scaled length (so area under the curve is molarity):



    And the package includes a function to automatically calculate the molar ratio of good inserts to bad adapter dimers in Illumina sequencing libraries.

    This is a work in progress so I would be grateful for any feedback.

  • #2
    Thanks!!!
    This is a neat idea.

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    • #3
      Made it to CRAN yet?

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      • #4
        Originally posted by Marc_Jones View Post
        Made it to CRAN yet?
        Considering that or Bioconductor. It doesn't have any Bioconductor dependencies so CRAN might be easier for everyone involved, but on the other hand some of the homebrew data structures might be better implemented with Bioconductor tools and I haven't looked into that yet.

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        • #5
          Hi I don't own a tapestation but am getting a qc file from a service company and would like to analyze them using bioanalyzeR.
          But when I try to plot I get an error saying
          "Error in rep(F, nrow(electrophoresis$data)) : invalid 'times' argument"
          I don't see a time column on data table.
          How should I tell the service company to export the data? I get a .cD1000 file with out a marker lane

          Do you have any plans on incorporating Qiaxcel data in the package?
          Thank you.
          Last edited by Him26; 01-26-2021, 06:02 PM.

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