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The code (and datasets) written for and used in the microbiome ML benchmark paper we're writing. The goal is to have this in the form of an actionable python package as soon as we're done.
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Benchmark of Supervised ML methods for the analysis of envicronmental microbiomes and a python package that is not named yet

Installation

See Instructions.

Organizational matters

Contribute to this Repository

Please coordinate contributions with Henning Schröder (henning.schroeder@planet-ai.de) or Theodor Sperlea (theodor.sperlea@io-warnemuende.de).

Branch structure

  • master: contains releases, merges only from devel (restricted access, merge allowed by Theo and Henning)
  • devel: development branch (restricted access, merge allowed by members)

Contribute a feature

  1. Create a branch based on the current devel branch with name scheme feature/coolstuff
  2. Do cool stuff and use descriptive commit messages
  3. Make a pull request into the devel branch and add a reviewer as well as a short description
  4. The merge is done by the reviewer (for quality control ;))

Methdods

see here

Datasets

see here

TODO

  • [Issue #1] Decide on a set of datasets that fit the scope (this will lead to decisions such as test/train, 10fold-cv or loocv)
  • [Issue #2] Decide on sets of methods that fit the scope
  • [Issue #5] implement everyhting with an eye on open publication
  • [Issue #3] Decide on a Licence
  • [Issue #4] write pyproject.toml for metadata and make ready for PIP# Benchmark of Supervised ML methods for the analysis of envicronmental microbiomes and a python package that is not named yet