Skill Claude CodeCodex
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
Skill Claude CodeCodex
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
Skill Claude CodeCodex
Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational…
Skill Claude CodeCodex
Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
Skill Claude CodeCodex
Automated hypothesis generation and testing using large language models. Use this skill when generating scientific hypotheses from datasets, combining literature insights with empirical data, testing hypotheses against observational data, or conducting systematic hypothesis exploration for research discovery in…
Skill Claude CodeCodex
Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develop predictions, propose mechanisms, for scientific inquiry across domains.
Skill Claude CodeCodex
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.
Skill Claude CodeCodex
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
Skill Claude CodeCodex
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological…
Skill Claude CodeCodex
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
Skill Claude CodeCodex
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and…
Skill Claude CodeCodex
Convert various file formats (PDF, Office documents, images, audio, web content, structured data) to Markdown optimized for LLM processing. Use when converting documents to markdown, extracting text from PDFs/Office files, transcribing audio, performing OCR on images, extracting YouTube transcripts, or processing…
Command Claude Code
Export the current Claude Code session to a timestamped folder with full conversation history, metadata, and statistics.
Command Claude Code
Export current Claude Code session for sharing or backup.
Command Claude Code
Import a cctrace session export into Claude Code.
Command Claude Code
Restore from pre-import snapshot after a failed or unwanted import.
jimmc414/claude-code-plugin-marketplace
Plugin Claude Code
Plugin marketplace listing 1 plugin: example-deployment.
jimmc414/claude-code-plugin-marketplace
Plugin Claude Code
Adversarial test generation that finds real bugs by inverting the reward structure.
jimmc414/claude-code-plugin-marketplace
Agent
Generates adversarial tests that expose real bugs through realistic but challenging inputs. Use when creating tests designed to find logic errors.
jimmc414/claude-code-plugin-marketplace
Agent
PROACTIVELY USE this agent to manage adversarial test generation. Coordinates the Generator and Validator in a feedback loop. Use when asked to generate adversarial tests or find bugs.
jimmc414/claude-code-plugin-marketplace
Agent
Validates adversarial tests using a 4-phase pipeline (Static Analysis, Dynamic Execution, Oracle Verification, Mutation Testing). Returns structured JSON verdict.
jimmc414/claude-code-plugin-marketplace
Skill Claude CodeCodex
Analyze code to identify explicit contracts, implicit usage patterns, and realistic boundary conditions. Contains concrete formulas for calculating input realism limits. Use before generating adversarial tests.
jimmc414/claude-code-plugin-marketplace
Skill Claude CodeCodex
Library of realistic adversarial attack vectors and anti-patterns to avoid. Contains examples of valid attacks and subtle gaming patterns to reject.
jimmc414/claude-code-plugin-marketplace
Plugin Claude Code
Collaborative planning commands with iterative requirements gathering. Ensures thorough understanding before implementation through structured Q&A sessions.