Owner

waldronlab

15 indexed repositories · View on GitHub

curatedMetagenomicData
Curated Metagenomic Data of the Human Microbiome

R · 161 stars
curatedTCGAData
Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

R · 46 stars
curatedMetagenomicDataCuration
Sample Metadata Curation for curatedMetagenomicData

R · 32 stars
TCGAutils
Toolbox package for organizing and working with TCGA data

R · 31 stars
BugSigDB
A microbial signatures database

PHP · 9 stars
CNVRanger
Functionality for CNV analysis

R · 8 stars
BugSigDBExports
BugSigDB data files

R · 5 stars
bugSigSimple
Simple exploratory analysis of curated microbe signatures

R · 4 stars
agent-protocol-standard
Standard to define citable scientific protocols for use by AI agents

Python · 3 stars
bedbaser
An R client for bedbase.org

R · 3 stars
imageFeatureTCGA

R · 2 stars
bioanalyzer-backend
Streamline BugSigDB curation with AI-powered scientific paper analysis. Automatically extracts essential microbiome study metadata from r...

Python · 2 stars
stormsmicrobiome
Versioning for the STORMS microbiome checklist

0 stars
agent-protocols
Waldron Lab AI agent protocols — a content node in the agent-protocol-standard federation

0 stars
curator-desk
Curator dashboard for reviewing BioAnalyzer predictions — sortable table, field-level feedback, submit via GitHub Issues

R · 0 stars

Beginner friendly Everything

Open All

Use omicidx to fill in missing BioProjects and run accessions Open

enhancement

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

waldronlab/curatedMetagenomicDataCuration#166 · Opened Sep 18, 2026
biomarker_value pattern rejects negatives, scientific notation and <0.01 Open

schema

Difficulty 1/5 Under an hour Newbie friendliness 88/100

waldronlab/curatedMetagenomicDataCuration#165 · Opened Sep 18, 2026
studies_status.csv splits on commas, so "Korea, Republic of" becomes two values Open

bug

waldronlab/curatedMetagenomicDataCuration#164 · 1 assignee · Opened Sep 18, 2026
age_group: dictionary says NCIT:C17600, curators used NCIT:C49685 Open

schema

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

waldronlab/curatedMetagenomicDataCuration#163 · Opened Sep 18, 2026
Ontology term IDs use NCIT_C… instead of NCIT:C…, in 24,385 cells Open

schema

Difficulty 4/5 3-5 days Newbie friendliness 72/100

waldronlab/curatedMetagenomicDataCuration#162 · Opened Sep 18, 2026
CI validator silently skips 11 curated studies (glob is *_sample.tsv only) Open

bug schema

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

waldronlab/curatedMetagenomicDataCuration#160 · Opened Sep 18, 2026
WenC_2017 with uncovered columns that are not uncurated_-prefixed and more Open

bug

waldronlab/curatedMetagenomicDataCuration#159 · 1 assignee · Opened Sep 18, 2026
Duplicated experiments become orphaned and do not appear on the main study page Open

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

waldronlab/BugSigDB#348 · Opened Sep 17, 2026
Study page 42278997 does not display study information or controls (Edit, History, Delete, and Add a new Experiment buttons) Open

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

waldronlab/BugSigDB#347 · Opened Sep 17, 2026
Content Discrepancies in v1.03: Duplicate titles and guidance mismatches (Items 1.2, 4.11, 4.12) Open

waldronlab/stormsmicrobiome#7 · 1 assignee · Opened Sep 17, 2026
Add a `validate-protocol` skill Open

enhancement

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

waldronlab/agent-protocol-standard#37 · Opened Sep 13, 2026
Add a `create-protocol` skill Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 72/100

waldronlab/agent-protocol-standard#35 · Opened Sep 13, 2026
Add an `update-protocol` skill Open

enhancement

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

waldronlab/agent-protocol-standard#36 · Opened Sep 13, 2026
Create searchable protocols dashboard (GitHub Pages) Open

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 Open

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 Open

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 Open

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 Open

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 Open

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 Open

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 Open

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 Open

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 Open

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 Open

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) Open

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 Open

atomic-protocol bioinformatics microbiome statistics

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

waldronlab/agent-protocols#23 · Opened Sep 12, 2026
Protocol: prevalence filtering of microbiome features Open

atomic-protocol good-first-protocol microbiome statistics

Difficulty 3/5 1-2 days Newbie friendliness 72/100

waldronlab/agent-protocols#22 · Opened Sep 12, 2026
Protocol: corpus-level curation statistics for BugSigDB (paper Table 1) Open

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

advanced atomic-protocol microbiome statistics

Difficulty 4/5 3-5 days Newbie friendliness 52/100

waldronlab/agent-protocols#20 · Opened Sep 12, 2026
Composite protocol: benchmark microbe set enrichment methods against each other Open

advanced blocked composite-protocol microbiome statistics

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

waldronlab/agent-protocols#19 · Opened Sep 12, 2026
Protocol: CBEA: competitive balances for taxonomic enrichment analysis against BugSigDB signatures Open

advanced atomic-protocol bioinformatics microbiome statistics

Difficulty 4/5 3-5 days Newbie friendliness 64/100

waldronlab/agent-protocols#18 · Opened Sep 12, 2026
Protocol: PADOG: pathway analysis with down-weighting of overlapping sets against BugSigDB signatures Open

advanced atomic-protocol bioinformatics microbiome statistics

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

waldronlab/agent-protocols#17 · Opened Sep 12, 2026
Protocol: Over-representation analysis of microbe sets against BugSigDB signatures Open

atomic-protocol bioinformatics microbiome statistics

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

waldronlab/agent-protocols#16 · Opened Sep 12, 2026
Protocol: resampling test for signature replicability within a condition Open

advanced atomic-protocol microbiome statistics

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

waldronlab/agent-protocols#15 · Opened Sep 12, 2026
Protocol: sample-size-weighted metasignature pooling by body site and condition Open

advanced atomic-protocol microbiome statistics

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

waldronlab/agent-protocols#14 · Opened Sep 12, 2026
Protocol: semantic similarity between signatures at mixed taxonomic levels Open

advanced atomic-protocol bioinformatics microbiome statistics

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

waldronlab/agent-protocols#13 · Opened Sep 12, 2026
Composite protocol: generate a hypothesis from BugSigDB, test it in individual-participant data Open

advanced blocked composite-protocol microbiome statistics

Difficulty 5/5 Over a week Newbie friendliness 38/100

waldronlab/agent-protocols#12 · Opened Sep 12, 2026
Protocol: assemble a case-control cohort from curatedMetagenomicData Open

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

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

waldronlab/agent-protocols#11 · Opened Sep 12, 2026
Composite protocol: systematic review of BugSigDB signatures for one condition Open

blocked composite-protocol microbiome statistics

Difficulty 5/5 Over a week Newbie friendliness 38/100

waldronlab/agent-protocols#10 · Opened Sep 12, 2026
Protocol: cluster and display a signature similarity matrix Open

atomic-protocol good-first-protocol microbiome statistics

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

waldronlab/agent-protocols#9 · Opened Sep 12, 2026
Protocol: Jaccard similarity between signatures at a single taxonomic level Open

atomic-protocol good-first-protocol microbiome statistics

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

waldronlab/agent-protocols#8 · Opened Sep 12, 2026
Protocol: Monte Carlo critical frequency for recurrent taxa across signatures Open

atomic-protocol microbiome statistics

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

waldronlab/agent-protocols#7 · Opened Sep 12, 2026
Protocol: taxon frequency table with a binomial test of reported direction Open

atomic-protocol good-first-protocol microbiome statistics

Difficulty 4/5 3-5 days Newbie friendliness 62/100

waldronlab/agent-protocols#6 · Opened Sep 12, 2026
Protocol: study characteristics table for a set of curated signatures Open

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

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

waldronlab/agent-protocols#5 · Opened Sep 12, 2026
Protocol: assemble and QC a BugSigDB signature subset for a condition Open

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

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

waldronlab/agent-protocols#4 · Opened Sep 12, 2026
Define authentication expectations for private federated nodes Open

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

waldronlab/agent-protocol-standard#25 · 1 comment · Opened Sep 11, 2026
Define a canonical fully-qualified name syntax for protocols Open

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

waldronlab/agent-protocol-standard#24 · 1 comment · Opened Sep 11, 2026
Support ad-hoc protocol repositories outside the central registry Open

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

waldronlab/agent-protocol-standard#23 · 1 comment · Opened Sep 11, 2026
Specify the registry schema and define trust_tier semantics Open

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

waldronlab/agent-protocol-standard#22 · 1 comment · Opened Sep 11, 2026
Check that the runner's field list matches the standard, and its own steps Open

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

waldronlab/agent-protocol-standard#16 · 1 comment · Opened Sep 11, 2026

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