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SOP 3. Core analyses

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Luke Thompson edited this page Mar 9, 2016 · 4 revisions

Core analyses

Alpha diversity: Calculated per sample, easily parallelizable Beta diversity: Daniel's parallel block UniFrac is way faster and should work for 7.5M tip tree Principal coordinates: Now works with up to 50k samples using conda installation of scipy Taxa summaries: Calculated per sample, easily parallelizable

Extended analyses

  • GitHub issues -- start here: https://github.com/biocore/emp/issues -- work on these, add more
  • Slides from old talks: https://github.com/biocore/emp/tree/master/presentations and Google Drive
  • IPython notebook for plots: Seaborn, Emperor, Qiime results
  • Group significance: Dependent on specific questions
  • Machine learning: Somewhat dependent on specific questions
  • Co-occurrence: Display on the VROOM with Juergen
  • Phylogenetic trees: ETE, display on the VROOM with Juergen
  • Other: Yoshiki and Jamie have code/ideas, Bobby Prill meta-analysis
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