Write a marimo notebook in a Python file in the right format.
R plotting conventions for Seurat/scRNA-seq: UMAP square plots (aspect.ratio=1, raster=FALSE), polychrome cluster colors, DimPlot/FeaturePlot settings, saving 300 DPI PNG, volcano plots with EnhancedVolcano, statistical comparisons with rstatix/ggpubr.
R Markdown formatting patterns: chunk display strategies (include=FALSE + inline R vs results='asis'), table rendering with knitr::kable, header hierarchy with tabsets, downloadable file embedding, and what to avoid (cat/print in visible chunks).
Sequencing read requirements and bcl2fastq base masks for 10x Genomics libraries: chemistry-specific BasesMaskCR values, ATAC I2 barcode requirement (capital I not lowercase y), Visium FFPE vs frozen R2 length difference.
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.
Fast, reproducible scientific Python environments with pixi - conda and PyPI unified
Compact Plotly visualization patterns. Express for quick plots, Graph Objects for control.
CLI application patterns for Python. Triggers on: cli, command line, typer, click, argparse, terminal, rich, console, terminal ui.