skillshelf

Install, deploy, find, organize, audit, and clean up agent skills with the `skl` (skillshelf) CLI — one canonical library, deployed on demand. Use when the user says "install this skill", "add a skill from GitHub", "deploy/activate these skills", "what skills do I have", "where is this skill deployed", "my skills are scattered", "tag/organize my skills", "remove a skill", "is this skill out of date", or mentions skillshelf / `skl`. Also when they say "skill" loosely about managing reusable agent instructions (not writing app code).

A demo multi-persona discussion skill. Three role-played experts — an optimist, a skeptic, and a moderator — debate a question and converge on a recommendation. Triggers: /sample-chatroom, "panel discussion", "debate this".

A demo authoring skill that produces a structured how-to guide with sections, callouts, and reference files. Use as an example of a multi-file skill with a README and a references/ directory. Triggers: /sample-guide, "write a guide", "how-to".

Deconstruct a vague term to its concrete usage. Use when a business or philosophical term is fuzzy and needs to be pinned down before reasoning with it.

Map collected artifacts to a checklist of required items and flag what is missing. Use when assembling or auditing an evidence package against a fixed set of requirements.

Pick a strong blog or social-post headline from a library of proven formulas. Given a topic, recommend the right formula, fill it, and explain why it fits. Use when writing or optimizing a post headline.

Polish a scientific manuscript for clarity and flow without changing claims. Tighten topic sentences, remove hedging, and enforce consistent terminology. Use when a draft is complete and needs a language pass before submission.

Build submission-grade Nature-family figures. Define the figure's conclusion and evidence logic first, then produce multi-panel SVG/PDF/TIFF with correct fonts, sizing, and colorblind-safe palettes. Use for manuscript figures and high-impact journal plots.

Search a codebase fast with ripgrep + structural queries, then summarize where a symbol is defined and used. Use when the user asks "where is X", "find all usages of Y", or wants a map of a feature across files.

Run quality control on bulk RNA-seq data — adapter trimming, FastQC, alignment-rate checks, and a per-sample QC summary table. Use when the user has raw FASTQ files and needs a QC pass before differential expression.

Cluster single-cell RNA-seq data and annotate cell types. Older copy that also ran batch integration with Harmony before clustering. Drifted from the bioinfo canonical version — kept here by an old project move.

Cluster single-cell RNA-seq data and annotate cell types. Covers normalization, HVG selection, PCA, neighbors, Leiden clustering, and marker-gene-based annotation. Use when the user has a cell-by-gene matrix and wants cell-type clusters.

Stage all changes, write a conventional-commit message, and push to the current branch's remote. Use when the user says "commit and push", "commit this", or finishes a unit of work and wants it saved upstream.

Legacy DESeq2 wrapper kept only for reference. Superseded by rnaseq-qc plus a dedicated differential-expression skill. Do not activate.