Refactor codebases using Design by Typed Holes methodology - iterative, test-driven refactoring with formal hole resolution, constraint propagation, and continuous validation.
Use when defining n, choosing statistical tests, correcting for multiple comparisons, and reporting error bars for a Cancer Cell (Cell Press) manuscript.
Use when writing the Cancer Cell (Cell Press) front matter — the Summary, eTOC blurb, Highlights, and graphical abstract.
Use when designing or auditing the experimental plan for a Cancer Cell (Cell Press) study — orthogonal validation across in vitro, in vivo, and human tumor systems, with controls,…
Use when running the final pre-submission preflight for Cancer Cell (Cell Press) — file completeness, STAR Methods / Key Resources Table, deposition accessions, statistics…
Clean up old tracking data and reset statistics
Query and analyze Claude Code session data from a remote server. Use when asked to inspect Claude Code sessions, view conversation history, check tool calls, track tasks, search…
Use to build Cell's mandatory STAR Methods — the Key Resources Table, the three Resource Availability subsections, Experimental Model and Subject Details, Method Details, and…
Use when targeting Cement and Concrete Research or deciding whether a cementitious-materials manuscript fits this venue.
Use when scrutinizing statistical inference for a 《经济学(季刊)》 (China Economic Quarterly, CEQ) manuscript — choosing and justifying the clustering level, handling weak instruments…
Systematic 4-phase debugging — root cause investigation, hypothesis testing, regression-guarded fix, mandatory bug doc.
Break LLM name defaults with external entropy. Use when character names cluster around statistical medians (Chen, Patel, Maya, Marcus), when cast has collision risks, or when…
ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discove — from…
Verify a cited empirical/numeric claim against an open mirror (aiXiv, OpenAlex, Semantic Scholar, the author's own copy) before citing it.
Use when designing the real-data validation of a 《中国管理科学》 (Chinese Journal of Management Science) manuscript — forecasting and financial-engineering strands: data provenance,…
Use when designing the numerical experiments and 算例 of a 《中国管理科学》 (Chinese Journal of Management Science) manuscript — grounded parameter calibration, an experiment matrix,…
Use when choosing the solution route and delivering the algorithm section of a 《中国管理科学》 (Chinese Journal of Management Science) manuscript — exact vs heuristic vs learning-based,…
Expert assistant for conducting remote experiments with Claude-Light - a web-accessible RGB LED and spectral sensor instrument for statistics, regression, optimization, a — from…
Expert assistant for conducting remote experiments with Claude-Light - a web-accessible RGB LED and spectral sensor instrument for statistics, regression, optimization, a — from…
Execute R code through RStudio via MCP. Use for R programming tasks, statistical analysis, data visualization, or setting up/troubleshooting the RStudio integration with Claude…
Connects to Clearscope API to generate content grades based on NLP term frequency analysis. Automates keyword research via Clearscope Research Reports endpoint and outputs…
Unified tool for calculating sample sizes for Diagnostic, Efficacy, Etiology, and Prognosis clinical studies.
Submit compact ClinicalTrials.gov API v2 requests for study search, metadata, enums, search areas, and field statistics.
Count lines of code, analyze codebase size and composition, compare code between versions. Use when the user asks about lines of code, codebase size, language breakdown, or code…
Generate comprehensive clonality statistics and diversity visualizations for TCR/BCR repertoire analysis.
Generate comprehensive clonality statistics and diversity visualizations for TCR/BCR repertoire analysis.
Analyzes AWS CloudTrail event logs via the Lookup Events API to detect anomalous IAM activity. Uses statistical baselining of API call patterns and flags unusual AssumeRole…
Use when after peak clustering has been performed on aligned GCIMS samples and a peak table matrix has been constructed, but the matrix contains NA values because some samples did…
Finds differentially expressed genes (markers) for clusters of T/B cells using Seurat's FindMarkers function.
Finds differentially expressed genes (markers) for clusters of T/B cells using Seurat's FindMarkers function.
Initialize a new AI co-mathematician research project. Use when the user wants to start a new math research investigation with AI agent support, or types "/co-math-init", "start a…
Render a compact status view of an AI co-mathematician research project — goals, active workstreams, blocked items, pending reviews, recent decisions.
Autonomous multi-agent code evolution system for optimization problems. Use when solving complex optimization problems (packing, geometry, scheduling, search) through evolutionary…
Deep codebase analysis to discover actual coding standards through statistical evidence. Use when analyzing naming conventions, import patterns, or detecting anti-patterns in…
Analyze codebase with tokei (fast line counts by language) and difft (semantic AST-aware diffs). Get quick project overview without manual counting.
Use when after normalization of a metabolomic feature matrix but before statistical testing, when you have both QC (technical replicate) and non-QC (study) samples and need to…
Diagnose, build, and repair the CogniForge Math Pipeline — the LangGraph 3-node StateGraph that handles BAC math questions.
Context and memory optimization skill for AI agents. Use when working on long conversations, multi-step tasks, coding sessions, research workflows, refactors, and situations where…
Use when when you have N-Me derivatized unsaturated sterol lipid structures (as SMILES or molecular formula) and need to predict MS/MS fragmentation patterns with…
Mathematically correct color system generation. Produces WCAG-compliant palettes, dark mode pairs, gradient smoothing, and dominant color extraction using LCH/LAB color math.
Use when deciding whether a result is COLT-shaped (Conference on Learning Theory) — a theorem-first learning-theory contribution — versus better routed to ALT, STOC/FOCS,…
Compare keyword sets between resume and job description. Returns match statistics including score, missing keywords, and intersection.
Use when refactoring existing code that has poor Big-O — nested loops, O(n^2)+ scans, repeated work, redundant allocations, blown memory, or stated symptoms like "this is slow on…
Build institutional-grade comparable company analyses with operating metrics, valuation multiples, and statistical benchmarking in Excel/spreadsheet format.
Use when designing or auditing the evaluation of an ACM CoNEXT paper — matching evidence to claim shape with real testbeds and deployments, honest and tuned baselines, measurement…
Deep spec analysis on a Confluence page. Reads page (+ children) via the confluence-as wrapper, produces a structured Spec Research Report with requirements, acceptance criteria,…
L1 trigger - audits consensus arithmetic for truncation, unused bounds, EMA direction, and threshold edge errors.
Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data.
Explains why studies on the same biomedical topic reach different or opposing conclusions by auditing differences in population, endpoint definition, sample source, assay or…
Use when designing or auditing experiments for a CoRL robot-learning paper — seeds and evaluation-episode counts, task-suite breadth, real-robot versus simulation evidence,…
Use when after applying one or more intensity drift correction strategies (Internal Standard correction, statistical drift correction, custom or weighted bracketing) within…
Use when after computing a correlation matrix (e.g., Pearson correlation across samples) on statistically significant LC-MS features, particularly when you need to inspect…
Use when when training a regularized deep neural network for molecular property regression (e.g., retention time prediction on the METLIN SMRT dataset with 80,038+ samples), use…
Count the total number of MCP tools in the Umbraco MCP Server project and provide a breakdown by collection.
Provides canonical entity counts from count-manifest.json. Use when agents need to reference how many agents, skills, instructions, or validators exist.
Decode a counteroffer after you resign — what the raise, promotion promise, or title bump really signals, the statistics-informed risks of staying, and a clear-eyed decision…
Use when after calculateDiffMeth() has been run on a methylBase object and you have a methylDiff object with q-values and methylation difference estimates.
Process CRISPR screening data to identify essential genes and hit candidates. Performs quality control, statistical analysis (RRA), and hit calling for pooled CRISPR screens…
End-to-end CRISPR screen analysis from FASTQ to hit genes. Orchestrates guide counting, QC, statistical analysis with MAGeCK, and hit calling with multiple methods.
Critique academic figures for print quality, accessibility, legibility, visual encoding, and statistical presentation.