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Write or fix a test in the Lyrion Dashboard's suite. Use this whenever a task adds a test, changes one, or asks why the suite fails — anything touching `tests/`. Covers the standalone-per-file scaffolding, the env-before-import rule, where to patch (the route/service the code under test imports), the cache-and-clock testing pattern, and how to run one test vs the whole suite. Reach for it any time you touch `tests/` so new tests match the existing shape instead of re-inventing setup.

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Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

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Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or pipeline filtering using ggalluvial, networkD3, plotly, and consort. Use when showing how entities move between categories across timepoints (cell states, drug response classes, patient flow through a trial) or filtering pipelines (variants filtered through QC stages).

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Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classifier scoring per-gene Bayes Factors via log-likelihood ratios over per-sgRNA fold changes, calibrated against CEGv2 core-essentials (Hart 2017 G3, ~684 genes) and NEGv1 non-essentials (Hart 2014, ~927 genes). Covers the fc + bf + pr workflow, the linear-extrapolation improvement over BAGEL1 truncation, multi-target off-target correction, tumor-suppressor sensitivity (BAGEL2 detects enrichment), and BF-to-FDR calibration (BF >6 ≈ FDR 0.05 from Hart 2017). Use when classifying essential vs non-essential genes, calibrating BAGEL2 thresholds against PR curves, identifying tumor suppressors alongside essentials, comparing BAGEL2 hits to MAGeCK / drugZ, or generating publication-quality essentiality calls.

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Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.

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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

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Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.

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Run the API contract workflow for public interface changes, compatibility constraints, contract tests, documentation, and review.

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Generates a commit in English following Conventional Commits based on staged changes

日本語の概要は準備中です。原文の説明を表示しています。

Run the API contract workflow for request/response shape changes, compatibility constraints, contract tests, documentation, and review.

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Use when creating database migrations, schema changes, seed data, or any SQL that modifies database structure. Covers Flyway naming conventions, versioning, and safe migration patterns.

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Run the database migration workflow for schema/data changes, operational sequencing, tests, and review.

日本語の概要は準備中です。原文の説明を表示しています。

Iteratively detects and auto-fixes technical debt in a codebase using three quality criteria from debt-analysis references: conditional branch simplification, encapsulation, and separation of concerns. Applies fixes directly to code, runs existing tests to verify no regressions, re-analyzes, and loops until all high-severity issues are resolved or max iterations (5) reached. Use this skill when you want to automatically improve code quality with real code changes, reduce technical debt systematically, or clean up code to meet quality standards. Trigger on phrases like "fix technical debt", "clean up code quality", "refactor and fix issues", "improve code quality automatically", "apply debt fixes", "fix code problems", "eliminate debt".

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Plan and execute Convex schema migrations safely, including adding fields, creating tables, and data transformations. Use when schema changes affect existing data.

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Full-stack Convex development guidelines covering React, Vite, TypeScript, mutations, auth, design system, and documentation practices. Use when building features, writing Convex functions, or making code changes in this project.

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Plans Convex schema and data migrations with widen-migrate-narrow and @convex-dev/migrations. Use for breaking schema changes, backfills, table reshaping, or zero-downtime rollouts.

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Project workflow for PRDs, task tracking, changelog sync, and documentation updates. Use for any non-trivial task that spans multiple steps, touches several files, changes architecture, or needs project tracking updates. Also activates with @update to sync task.md, changelog.md, and files.md after completing work.

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Critical Git safety rules to prevent destructive operations. Use whenever performing git operations, reverting changes, or managing commits. Prevents accidental loss of work.

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Improve test value and feedback cost when auditing slow, flaky, redundant or brittle tests; choosing tests during implementation; or reviewing test changes before a commit or PR. Keep ordinary implementation and pre-commit use scoped to the affected behavior, not a repository-wide audit.

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Read this before the first Google Drive, Docs, Sheets or Slides connector call whenever the task creates or changes a Google file. Use this skill whenever the user wants to create or change a Google Doc, Sheet or Slides file in their Google Drive. Triggers include: a request that names Google Docs, Sheets, Slides or Drive and asks to make, edit, format, copy or rename a file; a docs.google.com link with a request to change that file, even a one-line fix or suggested edits; and any follow-up change to a Google file from earlier in the chat, even "change it" or "add a tab". Includes helper scripts for document positions, cell ranges and slide layout. However, if the user asks for a doc, deck or spreadsheet without naming Google, or gives a Google file only as source material for something new, use Claude's own output type instead. Do NOT use for read-only questions about a Google file, or for Word, Excel, PowerPoint or PDF files.

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Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx) or Word templates (.dotx). Triggers include: any mention of Microsoft Word Documents, such as 'Word doc', 'word document', '.docx', '.dotx', 'microsoft doc'. Also use when extracting or reorganizing content from .docx or .dotx files, inserting or replacing images in documents, find-and-replace in Word files, working with tracked changes or comments, or converting content into a polished Word document. If the user asks for a deliverable as a Word or .docx file (to download, email or print), use this skill. However, if they ask for a document, page, report, memo, or notes WITHOUT naming a file format and the session offers Claude's own dedicated document or page skill or connector, use that instead, even if they will email or print it. Do NOT use for PDFs, spreadsheets, Google Docs, or coding unrelated to document generation.

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docs (editable docs people share and comment on; the default for any document, named as a doc or not: a document, report, proposal, resume, cover letter, letter, contract, policy, form, template, worksheet, essay, handbook, guide, how-to, cheat sheet, SOP or other writing to keep, share, collaborate on, send, submit, print or sign; a doc exports to Word, PDF, Markdown or Google Docs, so needing a file to send, attach, upload, submit or print is no reason to pick Word, and a file nobody asked for is a doc, not Word; a plan, comparison, summary or notes asked in chat stays in chat; a pasted claude.ai artifact link may be a doc: check with docs tools first; Word or another file format named, tracked changes wanted, or a .docx to change or use as a template → that format's skill): making one → if no docs-connector instructions are in context, call its `guide` (topic.instructions) first; then create the doc (headings only, no body) before any search, file read or plan, even with files attached.

日本語の概要は準備中です。原文の説明を表示しています。

Behavioral guidelines to reduce common LLM coding mistakes. Use when writing, reviewing, or refactoring code to avoid overcomplication, make surgical changes, surface assumptions, and define verifiable success criteria.

日本語の概要は準備中です。原文の説明を表示しています。