Milestones

List view

• Phase 7 — Publication

  The manuscript is written in Quarto. Figures and tables come from the notebooks, not copied by hand. The likely target journal is **Nature Protocols**; the section tasks below follow whatever structure the journal requires (checked in T41).

  No due date

  •0/8 issues closed
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• Phase 6 — Reproducibility setup (later)

  Deferred until the tools are known. Until then, each person notes the R packages and tools they use in their module README, and notebooks are rendered on their own.

  No due date

  •0/4 issues closed
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• Phase 5 — Analysis

  No due date

  •0/5 issues closed
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• Phase 4 — Integration

  No due date

  •0/3 issues closed
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• Phase 3 — Metabolomic preprocessing

  The metabolomics module follows the [Metabonaut](https://rformassspectrometry.github.io/Metabonaut/) tutorials (RforMassSpectrometry), mainly *End-to-end untargeted metabolomics workflow* and *Dataset investigation*. Each task names the tutorial section it corresponds to; deviations from the tutorial are explained in the notebook.

  No due date

  •0/11 issues closed
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• Phase 2 — Metagenomic preprocessing

  No due date

  •0/11 issues closed
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• Phase 1 — Data and metadata

  No due date

  •0/7 issues closed
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• Phase 0 — Getting started

  No due date

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