bfabricpy
Python interface to the B-Fabric laboratory information management system. Use when working with B-Fabric API for CRUD operations on samples, datasets, workunits, resources, or building B-Fabric applications and scripts.
bookdown
Cross-referencing in R Markdown documents using bookdown. Use when creating Rmd files that need references to figures, tables, equations, or sections. Triggers on requests for academic reports, technical documents, or any R Markdown with numbered cross-references.
general-agentic
Defensive epistemology protocol for coding agents. Rationalist principles applied to code: explicit predictions, notice confusion, verify before proceeding.
marimo-compact
Compact marimo notebook patterns. Reactive cells, UI elements, data visualization.
mixed-r-python-pipeline
Expert guidance for turning existing Snakemake analysis projects (with Snakefile + src/) into pip-installable CLI tools that can deploy the workflow to new projects. Use when the user has a working analysis project with Snakemake and R/Python scripts and wants to make it reusable/deployable. Creates CLI with init, validate, update, clean, info commands. Reference implementation at /Users/wolski/projects/ptm-pipeline.
phosphoproteomics-ptm-analysis
Guide for analyzing phosphoproteomics data using R, focusing on differential PTM abundance (DPA), differential PTM usage (DPU), and kinase enrichment analysis workflows.
pixi-package-manager
Fast, reproducible scientific Python environments with pixi - conda and PyPI unified
plotly-compact
Compact Plotly visualization patterns. Express for quick plots, Graph Objects for control.
plotly
Plotly visualization patterns for statistical and scientific charts. Use when creating interactive visualizations, statistical plots (scatter, box, violin, heatmaps), UpSet plots for set intersections, network graphs, or exporting figures to HTML/PNG/PDF/SVG formats. Covers both Plotly Express (high-level) and Graph Objects (low-level) APIs.
python-cli-patterns
CLI application patterns for Python. Triggers on: cli, command line, typer, click, argparse, terminal, rich, console, terminal ui.
python-style-guide-compact
Compact Python style guide. Key conventions for clean, typed, documented code.
python-style-guide
Comprehensive Python programming guidelines based on Google's Python Style Guide. Use when you needs to write Python code, review Python code for style issues, refactor Python code, or provide Python programming guidance. Covers language rules (imports, exceptions, type annotations), style rules (naming conventions, formatting, docstrings), and best practices for clean, maintainable Python code.
r-development
Modern R development practices emphasizing tidyverse patterns (dplyr 1.1 and later, native pipe, join_by, .by grouping), rlang metaprogramming, performance optimization, and package development. Use when you needs to write R code, create R packages, optimize R performance, or provide R programming guidance.
school-study-materials
Generate Kurzusammenfassungen (summaries), Lernziele (learning objectives), and Kontrollfragen (control questions) from school scripts.
scverse-compact
Compact single-cell analysis patterns with AnnData and Scanpy. Essential patterns for QC, preprocessing, clustering, and visualization.
scverse
Single-cell analysis patterns with AnnData and Scanpy. Use when working with single-cell RNA-seq data, creating or manipulating AnnData objects, performing quality control, normalization, dimensionality reduction, clustering, or visualization of single-cell datasets.
shell-scripting
Specialized knowledge of Bash and Zsh scripting, shell automation, command-line tools, and scripting best practices. Use when the user needs to write, debug, or optimize shell scripts, work with command-line tools, automate tasks with bash/zsh, or asks for shell script help.
snakemake-compact
Compact Snakemake workflow patterns. Keep rules short, complex logic in Python modules.