Issues

• [General] Final render and submission files

  publicationtrack: general
  microbiome/workflows#58 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 7 — Publication

• [General] Write the remaining sections and the Abstract

  publicationtrack: general
  microbiome/workflows#57 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 7 — Publication

• [General] Write the procedure and results sections

  publicationtrack: general
  microbiome/workflows#56 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 7 — Publication

• [General] Write the introductory sections

  publicationtrack: general
  microbiome/workflows#55 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 7 — Publication

• [General] Set up the bibliography

  good first issuepublicationtrack: general
  microbiome/workflows#54 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 7 — Publication

• [General] Add author information to the manuscript

  good first issuepublicationtrack: general
  microbiome/workflows#53 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 7 — Publication

• [General] Draft the paper outline in the manuscript

  publicationtrack: general
  microbiome/workflows#52 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 7 — Publication

• [General] Check the Nature Protocols requirements

  decisionpublicationtrack: general
  microbiome/workflows#51 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 7 — Publication

• [General] Render the manuscript automatically with GitHub Actions

  setuptrack: general
  microbiome/workflows#50 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 6 — Reproducibility setup (later)

• [Metagenomics] Pin the metagenomic processing setup

  setuptrack: metagenomics
  microbiome/workflows#49 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 6 — Reproducibility setup (later)

• [General] Set up DESCRIPTION for R dependencies

  setuptrack: general
  microbiome/workflows#48 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 6 — Reproducibility setup (later)

• [General] Set up the Quarto manuscript project

  setuptrack: general
  microbiome/workflows#47 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 6 — Reproducibility setup (later)

• [Integration] Compare the methods

  analysisdocstrack: integration
  microbiome/workflows#46 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 5 — Analysis

• [Integration] Analysis: cross-association between taxa and metabolites

  analysistrack: integration
  microbiome/workflows#45 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 5 — Analysis

• [Metabolomics] Exploratory analysis: metabolome

  analysistrack: metabolomics
  microbiome/workflows#44 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 5 — Analysis

• [Metagenomics] Exploratory analysis: metagenome

  analysistrack: metagenomics
  microbiome/workflows#43 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 5 — Analysis

• [Integration] Choose the integration methods

  analysisdecisiontrack: integration
  microbiome/workflows#42 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 5 — Analysis

• [Integration] Decide how to share the processed data

  decisiontrack: integration
  microbiome/workflows#41 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 4 — Integration

• [Integration] Validate the MultiAssayExperiment

  track: integration
  microbiome/workflows#40 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 4 — Integration

• [Integration] Build the MultiAssayExperiment

  track: integration
  microbiome/workflows#39 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 4 — Integration

• [Metabolomics] Save the final SummarizedExperiment

  track: metabolomics
  microbiome/workflows#38 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 3 — Metabolomic preprocessing

• [Metabolomics] MS2-based annotation (if MS2 data is available)

  track: metabolomics
  microbiome/workflows#37 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 3 — Metabolomic preprocessing

• [Metabolomics] MS1-based annotation

  track: metabolomics
  microbiome/workflows#36 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 3 — Metabolomic preprocessing

• [Metabolomics] QC-based feature filtering

  track: metabolomics
  microbiome/workflows#35 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 3 — Metabolomic preprocessing

• [Metabolomics] Normalisation

  track: metabolomics
  microbiome/workflows#34 · Filter by author TuomasBorman opened on Oct 15, 2026 · Phase 3 — Metabolomic preprocessing