writing-r-code

What problem does it solve?

It prevents brittle, outdated, or non-reproducible R code in scRNA-seq and Bioconductor/Seurat workflows by enforcing consistent project conventions and verifying package APIs before function calls.

Core Features & Use Cases

• Context7-verified package API calls: Perform required lookups before calling API-sensitive functions across Seurat, Bioconductor, and related ecosystem packages.
• Tidyverse-first, Seurat-correct coding patterns: Use dplyr pipelines for metadata operations while keeping Seurat analysis functions in Seurat-native syntax.
• Self-contained, executable R code chunks: Structure chunks with Libraries, Inputs, Processing, and Outputs so each chunk runs independently and writes checkpoints/figures reliably.
• Seurat v5 layer-based workflows: Apply layer conventions such as JoinLayers() and IntegrateLayers() for multi-sample integration and downstream steps.

Quick Start

Use the writing-r-code skill to write or revise an R pipeline for Seurat v5 that saves checkpoints and generates BadranSeq-based plots while verifying every API-sensitive function call via Context7.