agentic-skills

Use when renaming files, organising media assets, or establishing file naming standards for any project. Applies to images, documents, data files, and outputs. Enforces snake_case with descriptive names, ISO 8601 dates, and zero-padded sequential numbering.

Use when setting up a new R or bioinformatics analysis project, scaffolding directory structures, refactoring messy scripts into clean pipelines, or establishing project conventions. Use when the user says "init", "set up a project", "refactor these scripts", or "create a pipeline". Also use when reviewing whether an existing project follows these conventions.

Use when debugging Quarto (`.qmd`) notebooks chunk-by-chunk via auto-generated tryCatch runners. Triggers when a `quarto render` fails opaquely, when you need to surface every failing chunk in one pass rather than stop at the first error, when iteratively fixing analysis pipelines (Seurat / Bioconductor / GSEA / biomaRt / msigdbr / clusterProfiler), or when adopting an inherited notebook tree whose chunks no longer execute end-to-end. Workflow: parse the qmd → emit a sibling `.R` runner with one `tryCatch` per `{r}` chunk → run it → fix the source qmd → regenerate the runner → repeat until the PASS / FAIL / SKIP summary table is fully green; then commit the qmd fixes and do a final `quarto render`.

Use when creating or editing Quarto (.qmd) documents for scientific analysis. Use when writing analysis pipelines, bioinformatics workflows, or scientific notebooks. Use when structuring code chunks with surrounding documentation, rationale, or methodology descriptions.

Use when writing, editing, or reviewing R code in any project. Use when working with Seurat, Bioconductor, tidyverse, scRNA-seq pipelines, or any R-based analysis. Use when generating code chunks for QMD documents, R scripts, or interactive sessions.

Use when tailoring CVs and cover letters for job applications (academic or industry). Use when parsing job adverts, scaffolding application directories, drafting cover letters, or tailoring CVs to specific roles. Use when the user shares a job advert (text, URL, or PDF) and wants application documents produced.

Use when creating or maintaining a repository of recommendation letters for applications, especially Quarto-based .qmd letters rendered to PDF. Use for bootstrapping a new repo, adding a new institution folder, editing an existing letter, or rendering final PDFs from application-specific materials.

Use when creating, modifying, or maintaining R packages. Use when editing R/ source files, DESCRIPTION, NAMESPACE, roxygen2 documentation, tests, or CI workflows in an R package context. Use when adding functions, bumping versions, managing dependencies, or preparing releases.

Use when converting a markdown file produced by Claude into a rendered self-contained HTML document via Quarto. Triggers include requests to render md to html, convert markdown output to a polished document, or produce a shareable HTML from a markdown draft.

Use when creating lab notebook documentation, LabArchive entries, or detailed records for datasets, analysis pipelines, tools, packages, or educational content. Use when documenting a completed workflow, evaluating a new tool, recording literature notes, or creating reference documentation for a project.

Use when adding, editing, or publishing blog posts on the Hugo personal site at badran-elshenawy.netlify.app. Use when creating new series posts, rendering R Markdown to markdown, updating the README, or committing and pushing content. Applies to all work in the my_website repository.

Use when writing or editing .md, .rmd, or .qmd files. Apply when authoring lists, headings, or structured content rendered by pandoc — including Hugo (via hugodown), Quarto, or plain markdown pipelines. Enforces formatting patterns that ensure correct vertical rendering of bullet lists and other structural elements across all three document types.

Use when making git commits, writing commit messages, creating branches, or managing version control history. Use when the user asks to commit, when a task is complete and needs committing, or when reviewing commit message style. Also use when rebasing, squashing, or rewriting commit history.