waldronlab

Issues somebody may already be working on are listed last. List everything by date

• Cached access to the bulk metadata snapshot

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  Difficulty 4/5 3-5 days Newbie friendliness 22/100

  waldronlab/bedbaser#28 · Opened Nov 1, 2026

• Vignette: range queries across a set of BED files

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  Difficulty 2/5 1-3 hours Newbie friendliness 55/100

  waldronlab/bedbaser#29 · Opened Nov 1, 2026

• Wrap the exact metadata search endpoint

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  Difficulty 2/5 1-3 hours Newbie friendliness 62/100

  waldronlab/bedbaser#27 · Opened Nov 1, 2026

• Fetch a vector of BED ids as a named GRangesList

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  Difficulty 4/5 3-5 days Newbie friendliness 45/100

  waldronlab/bedbaser#26 · Opened Nov 1, 2026

• Range queries across a set of BED files

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  Difficulty 5/5 Over a week Newbie friendliness 22/100

  waldronlab/bedbaser#25 · Opened Nov 1, 2026

• build_manifest.py counts registered v2 samples as processed

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  Difficulty 3/5 1-2 days Newbie friendliness 62/100

  waldronlab/curatedMetagenomicDataCuration#178 · Opened Nov 1, 2026

• cMD4: ship-or-defer decision for 4.0.0 given release coverage

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  cmd4

  Difficulty 5/5 Over a week Newbie friendliness 8/100

  waldronlab/curatedMetagenomicData#350 · Opened Oct 31, 2026

• cMD4: refresh sampleMetadata from the curation repo before release

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  cmd4

  Difficulty 3/5 1-2 days Newbie friendliness 35/100

  waldronlab/curatedMetagenomicData#349 · Opened Oct 31, 2026

• cMD4: decide whether to expose the release's Olm-merged metadata tables

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  cmd4

  Difficulty 5/5 Over a week Newbie friendliness 10/100

  waldronlab/curatedMetagenomicData#348 · Opened Oct 31, 2026

• cMD4: add the HUMAnN data types when the HUMAnN datasets are published

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  cmd4

  Difficulty 4/5 3-5 days Newbie friendliness 18/100

  waldronlab/curatedMetagenomicData#347 · Opened Oct 31, 2026

• cMD4: attach a MetaPhlAn 4 row tree to relative_abundance objects

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  cmd4

  Difficulty 4/5 3-5 days Newbie friendliness 30/100

  waldronlab/curatedMetagenomicData#346 · Opened Oct 31, 2026

• makeSignatures() names discrete signatures "bugphyz:" (missing z)

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  Difficulty 2/5 1-3 hours Newbie friendliness 76/100

  waldronlab/bugphyzz#256 · Opened Oct 30, 2026

• ldaFunction(): score sign/magnitude biased toward the second class level (signed mean difference added to unsigned coefficient)

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  Difficulty 3/5 1-2 days Newbie friendliness 58/100

  waldronlab/lefser#104 · Opened Oct 28, 2026

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

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  protocol-revision

  Difficulty 3/5 1-2 days Newbie friendliness 64/100

  waldronlab/agent-protocols#58 · Opened Oct 24, 2026

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

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  protocol-revision

  Difficulty 3/5 1-2 days Newbie friendliness 53/100

  waldronlab/agent-protocols#57 · Opened Oct 24, 2026

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

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  protocol-revision

  Difficulty 2/5 1-3 hours Newbie friendliness 73/100

  waldronlab/agent-protocols#56 · Opened Oct 24, 2026

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

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  protocol-revision

  Difficulty 2/5 1-3 hours Newbie friendliness 74/100

  waldronlab/agent-protocols#55 · Opened Oct 24, 2026

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

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  protocol-revision

  Difficulty 4/5 3-5 days Newbie friendliness 45/100

  waldronlab/agent-protocols#54 · Opened Oct 24, 2026

• Template Materials style differs from the house style content repositories have settled on

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  Difficulty 1/5 1-3 hours Newbie friendliness 85/100

  waldronlab/agent-protocol-standard#57 · Opened Oct 23, 2026

• Template workflow tags <name>-v<version> when a protocol's version changes

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  Difficulty 4/5 3-5 days Newbie friendliness 55/100

  waldronlab/agent-protocol-standard#56 · Opened Oct 23, 2026

• Runner resolves dependencies from the composite's snapshot or its source, not the index

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  waldronlab/agent-protocol-standard#55 · Opened Oct 23, 2026

• Add `source` to cross-repository protocols_used entries and define same-repository by file presence

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  Difficulty 4/5 3-5 days Newbie friendliness 55/100

  waldronlab/agent-protocol-standard#54 · Opened Oct 23, 2026

• Index publishes the snapshot it describes: commit, per-entry sha256, protocol_url at the commit

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  Difficulty 4/5 3-5 days Newbie friendliness 48/100

  waldronlab/agent-protocol-standard#53 · Opened Oct 23, 2026

• Where do protocol test run records live?

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  Difficulty 5/5 Over a week Newbie friendliness 25/100

  waldronlab/agent-protocol-standard#44 · Opened Oct 18, 2026

• Protocol: Bray-Curtis dissimilarity matrix between samples

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  atomic-protocol microbiome statistics

  Difficulty 4/5 3-5 days Newbie friendliness 48/100

  waldronlab/agent-protocols#51 · Opened Oct 18, 2026

• Curator Desk daily-update workflow is invalid and has never run successfully

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  Difficulty 4/5 3-5 days Newbie friendliness 58/100

  waldronlab/bioanalyzer-backend#137 · Opened Sep 24, 2026

• v2 RAG pipeline only re-ranks the already-truncated 8k context, ignores summary settings, and never reads the cache

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  Difficulty 5/5 Over a week Newbie friendliness 42/100

  waldronlab/bioanalyzer-backend#135 · Opened Sep 24, 2026

• NCBI rate limiting is per-thread `sleep()`, so concurrent requests exceed NCBI's limit

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  Difficulty 4/5 3-5 days Newbie friendliness 55/100

  waldronlab/bioanalyzer-backend#134 · Opened Sep 24, 2026

• API has no authentication; `/qa` and `/analyze-url` let any caller spend LLM budget and choose the model

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  Difficulty 5/5 Over a week Newbie friendliness 28/100

  waldronlab/bioanalyzer-backend#132 · Opened Sep 24, 2026

• Structured extraction runs at temperature 0.7, so results aren't reproducible

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  Difficulty 3/5 1-2 days Newbie friendliness 74/100

  waldronlab/bioanalyzer-backend#131 · Opened Sep 24, 2026

• Remove leftover `taxa_level` field from URL-analysis schemas

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  Difficulty 3/5 1-2 days Newbie friendliness 78/100

  waldronlab/bioanalyzer-backend#130 · Opened Sep 24, 2026

• target_condition mismatch between *_sample.tsv and *_study.tsv

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  bug

  Difficulty 3/5 1-2 days Newbie friendliness 68/100

  waldronlab/curatedMetagenomicDataCuration#167 · Opened Sep 22, 2026

• Use omicidx to fill in missing BioProjects and run accessions

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  enhancement

  Difficulty 4/5 3-5 days Newbie friendliness 50/100

  waldronlab/curatedMetagenomicDataCuration#166 · 1 comment · Opened Sep 18, 2026

• studies_status.csv splits on commas, so "Korea, Republic of" becomes two values

  May be free again @lwaldron claimed this 43 days ago, and no pull request is open. Open

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  bug

  waldronlab/curatedMetagenomicDataCuration#164 · 1 assignee · Opened Sep 18, 2026

• age_group: dictionary says NCIT:C17600, curators used NCIT:C49685

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  schema

  Difficulty 2/5 1-3 hours Newbie friendliness 68/100

  waldronlab/curatedMetagenomicDataCuration#163 · Opened Sep 18, 2026

• Content Discrepancies in v1.03: Duplicate titles and guidance mismatches (Items 1.2, 4.11, 4.12)

  May be free again @cmirzayi claimed this 45 days ago, and no pull request is open. Open

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  waldronlab/stormsmicrobiome#7 · 1 assignee · Opened Sep 17, 2026

• Create searchable protocols dashboard (GitHub Pages)

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  Difficulty 4/5 3-5 days Newbie friendliness 35/100

  waldronlab/agent-protocol-standard#33 · Opened Sep 13, 2026

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

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  advanced blocked composite-protocol microbiome statistics

  Difficulty 5/5 Over a week Newbie friendliness 35/100

  waldronlab/agent-protocols#34 · Opened Sep 12, 2026

• Protocol: ANOSIM on a community distance matrix

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  atomic-protocol microbiome statistics

  Difficulty 3/5 1-2 days Newbie friendliness 74/100

  waldronlab/agent-protocols#33 · Opened Sep 12, 2026

• Protocol: PERMANOVA on a community distance matrix

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  atomic-protocol microbiome statistics

  Difficulty 4/5 3-5 days Newbie friendliness 68/100

  waldronlab/agent-protocols#32 · Opened Sep 12, 2026

• Protocol: random forest classification of microbiome profiles

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  atomic-protocol machine-learning microbiome

  Difficulty 4/5 3-5 days Newbie friendliness 68/100

  waldronlab/agent-protocols#31 · Opened Sep 12, 2026

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

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  atomic-protocol machine-learning statistics

  Difficulty 4/5 3-5 days Newbie friendliness 68/100

  waldronlab/agent-protocols#30 · Opened Sep 12, 2026

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

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  atomic-protocol data-curation microbiome

  Difficulty 4/5 3-5 days Newbie friendliness 65/100

  waldronlab/agent-protocols#29 · Opened Sep 12, 2026

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

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  atomic-protocol bioinformatics microbiome

  Difficulty 4/5 3-5 days Newbie friendliness 68/100

  waldronlab/agent-protocols#28 · Opened Sep 12, 2026

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

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  advanced blocked composite-protocol statistics

  Difficulty 4/5 3-5 days Newbie friendliness 48/100

  waldronlab/agent-protocols#27 · Opened Sep 12, 2026

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

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  advanced atomic-protocol statistics

  Difficulty 4/5 3-5 days Newbie friendliness 68/100

  waldronlab/agent-protocols#26 · Opened Sep 12, 2026

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

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  advanced atomic-protocol microbiome statistics

  Difficulty 4/5 3-5 days Newbie friendliness 68/100

  waldronlab/agent-protocols#25 · Opened Sep 12, 2026

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

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  advanced atomic-protocol microbiome statistics

  Difficulty 5/5 Over a week Newbie friendliness 45/100

  waldronlab/agent-protocols#24 · Opened Sep 12, 2026

• Protocol: centred log-ratio transformation of compositional abundances

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  atomic-protocol bioinformatics microbiome statistics

  Difficulty 4/5 3-5 days Newbie friendliness 74/100

  waldronlab/agent-protocols#23 · Opened Sep 12, 2026

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

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  atomic-protocol data-curation good-first-protocol microbiome

  Difficulty 4/5 3-5 days Newbie friendliness 70/100

  waldronlab/agent-protocols#21 · Opened Sep 12, 2026