result-checks

Plugin result-checks from marketplace agentic-research-toolkit in ChenHsieh/agentic-research-toolkit. Commands read from the repo's manifest — 20 days ago.

Skills (11)

• accession-paper-crosswalk

  Link a sequence-data accession to the paper that describes it, and a paper to the data it deposited - covering BioProject (PRJNA/PRJEB/PRJDB), SRA (SRP/SRX/SRR/SRS), BioSample (SAMN), and GEO (GSE) identifiers. Handles the alias expansion that makes or breaks the search, routes around NCBI's near-em

• agent-playbook

  Rules for an agent doing research work. Use at the start of any analysis, job submission, reproduction or delegation, and again before reporting a result, or when unsure whether a result is done, wrong, or not yet measured.

• design-confound-audit

  Determine which questions a dataset's design can actually answer, before any model is fit. Cross-tabulates the factor of interest against every nuisance factor to find perfect confounding (a factor fully nested inside another cannot be separated from it by any statistical method), cells below an inf

• ecosystem-mapper

  Map research fields, funding landscapes, and innovation ecosystems as interactive network graphs. Use this skill whenever the user wants to understand: who funds what in a field, who does research on what, how money flows through an academic or industry sector, which organizations dominate a space,

• ml-genomics-best-practices

  A checklist-driven workflow for running reproducible, defensible ML experiments in genomics. Enforces anti-circularity, class balance audit, LR baselines, bootstrap CIs, permutation tests, proper feature leakage prevention, and standardized reporting. Invoke whenever building a classification or reg

• result-autopsy

  Adversarially audit a result you have already produced, before a reviewer or a collaborator does it for you. Given a finding, a results file, or a claim in a draft, this executes the checks most likely to kill it - shared variables on both sides of a comparison, censoring that points the same way as

• scientific-schematics

  Create publication-quality scientific workflow diagrams as interactive HTML files with one-click SVG export for Figma. Use this skill whenever the user wants to build or recreate a flowchart, decision tree, pipeline schematic, methodology diagram (CONSORT, PRISMA), biological pathway, or any scienti

• second-opinion-concordance

  Re-derive a set of calls with a methodologically independent second method and mine the disagreements, which are the actual product. Covers choosing a method that fails differently from the first (not a parameter variant of it), running both over the same entities, building a concordance table, and

• statistic-null

  Give a derived summary statistic its own null distribution before believing anything it says. For any scalar computed from data - concentration, peakiness, enrichment ratio, importance mass, divergence, specificity, clustering score - construct a null that preserves everything except the claimed str

• tikz-figures

  Build publication-quality figures with TikZ/pgfplots - manuscript figures whose fonts must match the body text, pipeline and architecture schematics, or any figure that should regenerate from a data file instead of being redrawn by hand. Routes to a reusable template directory rather than writing pg

• trait-gene-miner

  Systematic workflow for mining experimentally validated genes associated with a biological trait from literature and ontology databases, with an interactive HTML dashboard output linking to source databases. Use whenever a user wants to collect, curate, or systematically identify genes linked to a p

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