Issues

• humann4 protocols: list the data each step consumes under Materials, then tier its conditions

  protocol-revision
  waldronlab/agent-protocols#59 · Filter by author lwaldron opened on Oct 24, 2026
  

• independent-filtering-variance: tier two Materials conditions and retire the validation step

  protocol-revision
  waldronlab/agent-protocols#58 · Filter by author lwaldron opened on Oct 24, 2026

• jaccard-signature-similarity: tier the Materials conditions and settle the taxonomy-coverage tension

  protocol-revision
  waldronlab/agent-protocols#57 · Filter by author lwaldron opened on Oct 24, 2026

• cbea-signature-enrichment: tier the Materials conditions and move four from Steps

  protocol-revision
  waldronlab/agent-protocols#56 · Filter by author lwaldron opened on Oct 24, 2026

• prevalence-filtering: move Step 2 conditions into Materials and tier them

  protocol-revision
  waldronlab/agent-protocols#55 · Filter by author lwaldron opened on Oct 24, 2026

• Bring existing protocols to ADR 0017: conditions on inputs live in Materials with must or should

  protocol-revision
  waldronlab/agent-protocols#54 · Filter by author lwaldron opened on Oct 24, 2026

• Protocol: Bray-Curtis dissimilarity matrix between samples

  atomic-protocolmicrobiomestatistics
  waldronlab/agent-protocols#51 · Filter by author lwaldron opened on Oct 18, 2026

• Protocol: Shannon diversity of a single sample

  atomic-protocolmicrobiomestatistics
  waldronlab/agent-protocols#50 · Filter by author lwaldron opened on Oct 18, 2026

• Composite protocol: cross-study meta-analysis of a host covariate in curatedMetagenomicData

  advancedblockedcomposite-protocolmicrobiomestatistics
  waldronlab/agent-protocols#34 · Filter by author lwaldron opened on Sep 12, 2026

• Protocol: ANOSIM on a community distance matrix

  atomic-protocolmicrobiomestatistics
  waldronlab/agent-protocols#33 · Filter by author lwaldron opened on Sep 12, 2026

• Protocol: PERMANOVA on a community distance matrix

  atomic-protocolmicrobiomestatistics
  waldronlab/agent-protocols#32 · Filter by author lwaldron opened on Sep 12, 2026

• Protocol: random forest classification of microbiome profiles

  atomic-protocolmachine-learningmicrobiome
  waldronlab/agent-protocols#31 · Filter by author lwaldron opened on Sep 12, 2026

• Protocol: leave-one-dataset-out cross-study validation

  atomic-protocolmachine-learningstatistics
  waldronlab/agent-protocols#30 · Filter by author lwaldron opened on Sep 12, 2026

• Protocol: derive a reference species set for a body site or sample group by prevalence

  atomic-protocoldata-curationmicrobiome
  waldronlab/agent-protocols#29 · Filter by author lwaldron opened on Sep 12, 2026

• Protocol: compute the oral-to-gut enrichment score for new samples

  atomic-protocolbioinformaticsmicrobiome
  waldronlab/agent-protocols#28 · Filter by author lwaldron opened on Sep 12, 2026

• Protocol: two-stage hierarchical meta-analysis across diseases

  advancedblockedcomposite-protocolstatistics
  waldronlab/agent-protocols#27 · Filter by author lwaldron opened on Sep 12, 2026

• Protocol: random-effects meta-analysis with the Paule-Mandel heterogeneity estimator

  advancedatomic-protocolstatistics
  waldronlab/agent-protocols#26 · Filter by author lwaldron opened on Sep 12, 2026

• Protocol: Fisher-Z transformed partial correlations for continuous exposures

  advancedatomic-protocolmicrobiomestatistics
  waldronlab/agent-protocols#25 · Filter by author lwaldron opened on Sep 12, 2026

• Protocol: per-dataset covariate-adjusted effect sizes (standardized mean difference)

  advancedatomic-protocolmicrobiomestatistics
  waldronlab/agent-protocols#24 · Filter by author lwaldron opened on Sep 12, 2026

• Protocol: centred log-ratio transformation of compositional abundances

  atomic-protocolbioinformaticsmicrobiomestatistics
  waldronlab/agent-protocols#23 · Filter by author lwaldron opened on Sep 12, 2026

• Protocol: corpus-level curation statistics for BugSigDB (paper Table 1)

  atomic-protocoldata-curationgood-first-protocolmicrobiome
  waldronlab/agent-protocols#21 · Filter by author lwaldron opened on Sep 12, 2026

• Protocol: microbe co-occurrence and mutual exclusivity across signatures

  advancedatomic-protocolmicrobiomestatistics
  waldronlab/agent-protocols#20 · Filter by author lwaldron opened on Sep 12, 2026

• Composite protocol: benchmark microbe set enrichment methods against each other

  advancedblockedcomposite-protocolmicrobiomestatistics
  waldronlab/agent-protocols#19 · Filter by author lwaldron opened on Sep 12, 2026

• Protocol: PADOG: pathway analysis with down-weighting of overlapping sets against BugSigDB signatures

  advancedatomic-protocolbioinformaticsmicrobiomestatistics
  waldronlab/agent-protocols#17 · Filter by author lwaldron opened on Sep 12, 2026

• Protocol: Over-representation analysis of microbe sets against BugSigDB signatures

  atomic-protocolbioinformaticsmicrobiomestatistics
  waldronlab/agent-protocols#16 · Filter by author lwaldron opened on Sep 12, 2026