sajor2000/methodsmith

sajor2000/methodsmith · AGENTS.md

sajor2000/methodsmith · CLAUDE.md

sajor2000/methodsmith · plugins/coding-tutor/skills/coding-tutor/SKILL.md · Personalized coding tutorials that build on your existing knowledge and use your actual codebase for examples. Creates…

sajor2000/methodsmith · plugins/methodsmith/AGENTS.md

sajor2000/methodsmith · plugins/methodsmith/skills/method-adversarial-review/SKILL.md · Challenges a high-stakes analysis diff or plan with an adversarial pass and, when available, a cross-model…

sajor2000/methodsmith · plugins/methodsmith/skills/method-anti-slop/SKILL.md · Detects and removes generic AI-writing tells from finished scientific prose, keeping passive Methods voice. Use when…

sajor2000/methodsmith · plugins/methodsmith/skills/method-brainstorm/SKILL.md · Explores a research or analysis idea, compares study designs, and scopes requirements before planning. Use when the…

sajor2000/methodsmith · plugins/methodsmith/skills/method-checklist/SKILL.md · Selects EQUATOR reporting guidelines (CONSORT, STROBE, RECORD, PRISMA, TRIPOD+AI, TARGET, STARD, CLAIM) for a study…

sajor2000/methodsmith · plugins/methodsmith/skills/method-citations/SKILL.md · Builds evidence-traceable citations from PubMed and Paperclip into a DOCX with editable Zotero fields. Use when adding…

sajor2000/methodsmith · plugins/methodsmith/skills/method-clean-branches/SKILL.md · Deletes local git branches whose upstream is gone, and their worktrees, after confirmation. Use when the user asks to…

sajor2000/methodsmith · plugins/methodsmith/skills/method-clif-meta-analysis/SKILL.md · Plans formal R/Python meta-analysis. Use when pooling CLIF site effects or conducting a literature systematic review.

sajor2000/methodsmith · plugins/methodsmith/skills/method-clif-template/SKILL.md · Initializes or audits a CLIF analysis repo against the official CLIF Project Template, with PHI and output safeguards…

sajor2000/methodsmith · plugins/methodsmith/skills/method-clif/SKILL.md · Applies CLIF (Common Longitudinal ICU data Format) rules: mCIDE versions, Parquet, UTC datetimes, no-PHI outputs. Use…

sajor2000/methodsmith · plugins/methodsmith/skills/method-cohort/SKILL.md · Defines a reproducible study cohort: inclusion/exclusion, index event, pinned concepts, SQL, waterfall counts. Use when…

sajor2000/methodsmith · plugins/methodsmith/skills/method-commit/SKILL.md · Creates a focused conventional git commit that keeps raw data, PHI, and large outputs out of version control. Use when…

sajor2000/methodsmith · plugins/methodsmith/skills/method-compound-refresh/SKILL.md · Audits docs/solutions learnings for drift, then keeps, updates, merges, replaces, or marks them stale. Use when the…

sajor2000/methodsmith · plugins/methodsmith/skills/method-compound/SKILL.md · Records a validated analytical approach, methods decision, or reusable data-science pattern in docs/solutions. Use when…

sajor2000/methodsmith · plugins/methodsmith/skills/method-data-qa/SKILL.md · Profiles columns or runs a GO/NO-GO data-quality gate on an extract before SAP finalization, modeling, or unblinding…

sajor2000/methodsmith · plugins/methodsmith/skills/method-debug/SKILL.md · Reproduces, traces, and fixes failing analysis code, pipelines, or tests by finding the cause first. Use when the user…

sajor2000/methodsmith · plugins/methodsmith/skills/method-doc-review/SKILL.md · Reviews plans, SAPs, protocols, and manuscripts for clarity, completeness, and scope with persona reviewers. Use when…

sajor2000/methodsmith · plugins/methodsmith/skills/method-evidence-map/SKILL.md · Builds a source-backed evidence map for a biomedical question from PubMed, optionally deepened with Paperclip full…

sajor2000/methodsmith · plugins/methodsmith/skills/method-extract/SKILL.md · Extracts methods, cohorts, endpoints, models, and assumptions from retrieved papers for SAP justification. Use when…

sajor2000/methodsmith · plugins/methodsmith/skills/method-fabric/SKILL.md · Routes Microsoft Fabric work (OneLake, Lakehouse, Warehouse, PySpark, Data Factory, Direct Lake, Fabric ML, KQL) with…

sajor2000/methodsmith · plugins/methodsmith/skills/method-figure/SKILL.md · Creates and validates publication figures (ggplot2, matplotlib) with a journal-neutral clinical style and manifest. Use…

sajor2000/methodsmith · plugins/methodsmith/skills/method-genome-build/SKILL.md · Pins genome build, annotation release, contig naming, and liftover for genomics data. Use when the user mentions…

sajor2000/methodsmith · plugins/methodsmith/skills/method-grill/SKILL.md · Interviews the user one question at a time to stress-test a study's goal, hypothesis, data, analysis, and journal…

sajor2000/methodsmith · plugins/methodsmith/skills/method-handoff/SKILL.md · Creates or resumes a portable continuity record for a data-science task, keeping SAP and real-data gates. Use when work…

sajor2000/methodsmith · plugins/methodsmith/skills/method-ideate/SKILL.md · Generates and ranks grounded research or analysis ideas from repo, literature, or topic context. Use when the user asks…

sajor2000/methodsmith · plugins/methodsmith/skills/method-language-detect/SKILL.md · Detects R, Python, or mixed-language signals in repo files and emits a language handoff. Use when a skill needs…

sajor2000/methodsmith · plugins/methodsmith/skills/method-lit-search/SKILL.md · Routes a literature request to PubMed, full-text evidence mapping, or authoritative web sources. Use when the user…

sajor2000/methodsmith · plugins/methodsmith/skills/method-marimo/SKILL.md · Creates, edits, validates, and reviews marimo reactive Python notebooks (UI widgets, PEP 723, export). Use when working…

sajor2000/methodsmith · plugins/methodsmith/skills/method-meta-analysis/SKILL.md · Pools literature effects with REML/Hartung-Knapp. Use when power or a SAP needs a cited effect-size assumption and…

sajor2000/methodsmith · plugins/methodsmith/skills/method-ml-track/SKILL.md · Adds reproducible ML experiment tracking (data hashes, splits, metrics, SAP links) with MLflow, W&B, DVC, or an offline…

sajor2000/methodsmith · plugins/methodsmith/skills/method-model-card/SKILL.md · Generates a clinical model card: intended use, data, performance with intervals, calibration, fairness, limits. Use…

sajor2000/methodsmith · plugins/methodsmith/skills/method-model-choice/SKILL.md · Chooses and justifies the statistical model (regression, mixed/GEE, survival, causal, prediction, Bayesian) after the…

sajor2000/methodsmith · plugins/methodsmith/skills/method-notebook-edit/SKILL.md · Edits existing Jupyter .ipynb notebooks with cell anchors, backups, and metadata-preserving writes. Use when the user…

sajor2000/methodsmith · plugins/methodsmith/skills/method-notebook-standards/SKILL.md · Sets the structure and documentation contract for new or extended marimo, Jupyter, R Markdown, and Quarto notebooks…

sajor2000/methodsmith · plugins/methodsmith/skills/method-numbers/SKILL.md · Locks manuscript numbers to an analysis-written registry; a fail-closed gate traces each to its SAP output, script…

sajor2000/methodsmith · plugins/methodsmith/skills/method-omics-qc/SKILL.md · Runs sequencing and omics QA: FASTQ, BAM/CRAM, VCF, count matrices, methylation arrays, sample swaps, batch…

sajor2000/methodsmith · plugins/methodsmith/skills/method-optimize/SKILL.md · Runs bounded, metric-scored experiment loops to improve a model, prompt, or pipeline without touching the test set. Use…

sajor2000/methodsmith · plugins/methodsmith/skills/method-phenotype/SKILL.md · Validates a computable phenotype against chart review: 2x2 table, PPV, NPV, sensitivity, specificity, Wilson intervals…

sajor2000/methodsmith · plugins/methodsmith/skills/method-plan/SKILL.md · Creates the durable plan for data-science work: an implementation plan or, for studies, a statistical analysis plan…

sajor2000/methodsmith · plugins/methodsmith/skills/method-power/SKILL.md · Calculates sample size and power for clinical, survival, cluster, and prediction-model studies, with a script, sweep…

sajor2000/methodsmith · plugins/methodsmith/skills/method-pr/SKILL.md · Commits, pushes, and opens or updates a pull request with a value-first body, keeping data and PHI out. Use when the…

sajor2000/methodsmith · plugins/methodsmith/skills/method-prereg/SKILL.md · Generates preregistration and registry content for OSF, ClinicalTrials.gov, PROSPERO, or a study protocol. Use when the…

sajor2000/methodsmith · plugins/methodsmith/skills/method-presubmit/SKILL.md · Runs the final gate on a manuscript, abstract, cover letter, or grant: section discipline, voice, and anti-slop passes…

sajor2000/methodsmith · plugins/methodsmith/skills/method-pubmed/SKILL.md · Searches PubMed/MEDLINE via E-utilities with MeSH-aware queries into a PMID and abstract CSV. Use when the user…

sajor2000/methodsmith · plugins/methodsmith/skills/method-question/SKILL.md · Turns one chosen biomedical study idea into PICO, FINER, a hypothesis, and PubMed-query YAML. Use when the user wants…

sajor2000/methodsmith · plugins/methodsmith/skills/method-r/SKILL.md · Routes R work: analysis design, tidyverse, event-study DiD, packages, testthat, CRAN, profiling, targets. Use when a…