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‘SRS’ R Package and ‘q2-srs’ QIIME 2 Plugin: Normalization of Microbiome Data Using Scaling with Ranked Subsampling (SRS)

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  • معلومة اضافية
    • بيانات النشر:
      Multidisciplinary Digital Publishing Institute
    • الموضوع:
      2021
    • Collection:
      MDPI Open Access Publishing
    • الموضوع:
    • نبذة مختصرة :
      Several ecological data types, especially microbiome count data, are commonly sample-wise normalized before analysis to correct for sampling bias and other technical artifacts. Recently, we developed an algorithm for the normalization of ecological count data called ‘scaling with ranked subsampling (SRS)’, which surpasses the widely adopted ‘rarefying’ (random subsampling without replacement) in reproducibility and in safeguarding the original community structure. Here, we describe an implementation of the SRS algorithm in the ‘SRS’ R package and the ‘q2-srs’ QIIME 2 plugin. We also provide accessory functions for dataset exploration to guide the choice of parameters for SRS.
    • File Description:
      application/pdf
    • Relation:
      Applied Microbiology; https://dx.doi.org/10.3390/app112311473
    • الرقم المعرف:
      10.3390/app112311473
    • الدخول الالكتروني :
      https://doi.org/10.3390/app112311473
    • Rights:
      https://creativecommons.org/licenses/by/4.0/
    • الرقم المعرف:
      edsbas.A0473DC