Results for “changes”

Deprecate APIs, features, or systems safely — announce, migrate consumers, sunset on a timeline, and document alternatives. Load when removing an old API, migrating users between implementations, sunsetting a feature, or the user asks about deprecation policy, migration guides, or breaking changes. Not for deleting dead code with zero consumers (use code-simplification). Distinct from meta `deprecate-skill` (skill library retirement).

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Complete migration guide from Prisma ORM v6 to v7 covering all breaking changes. Use when upgrading Prisma versions, encountering v7 errors, or migrating existing projects. Triggers on "upgrade to prisma 7", "prisma 7 migration", "prisma-client generator", "driver adapter required".

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Sync delta specs from a change to main specs. Use when the user wants to update main specs with changes from a delta spec, without archiving the change.

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Create branch, atomic commits, push, and open a pull request with terse, exact messages. Conventional branch + commit format. PR title ≤70 chars, body says "why", not "what". Use when the user says "create pr", "create pullrequest", "create pull request", "make pr", "open pr", "open pullrequest", "open pull request", "submit pr", "raise pr", "/create-pr", or asks to ship/send changes as a pull request (PR/pullrequest/pull-request, any spelling).

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Generate a single unified changelog from git history that works for everyone in the company (managers and non-tech colleagues as well as developers). Outputs Slack mrkdwn so it can be pasted straight into Slack. Defaults to Slovak (English only on explicit request) and to comparing the release branch (main) against develop to show unreleased changes; also supports date ranges like "today", "yesterday", "last week", or an explicit git range. User-invoked only via /changelog.

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Create atomic git commits with terse, exact Conventional Commits messages. Cuts noise, preserves intent. Subject ≤50 chars. Body only when "why" isn't obvious. Use when the user says "commit", "commit this", "/commit", or asks to stage and commit changes.

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Verify a code change end-to-end in the current worktree: identify what changed, run the relevant tests, get the app running, drive a browser over the affected areas, and report a verdict with screenshots. Generic across project types (Laravel/Herd, Node/bun, frontend, CLI, library). Use when the user wants to verify/QA/smoke-test a change, check that a PR or branch works, validate uncommitted work, or says "/flow", "verify this change", "does this PR work", "test and click through this". Optional target: PR number/URL, branch/ref, or worktree path; default is the current working changes.

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Implement several variations of a design directly inside the running app, on the real page/route, with a live switcher to toggle between them in the browser, then recommend one and fold the winner into the real code. Variants are real implementations judged against real data, layout, and density (not an isolated mockup). Use this skill whenever the user wants to try design options live in the app, prototype changes directly on a real page, add a variant switcher, compare layouts in-context, asks to "build a few versions of this page", "try variants on the real screen", "switch between designs in the app", "implement this with a toggle", or says "real-prototype this". For a safe standalone .html copy that never touches the app, use the prototype skill instead.

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Automatically creates user-facing changelogs from git commits by analyzing commit history, categorizing changes, and transforming technical commits into clear, customer-friendly release notes. Turns hours of manual changelog writing into minutes of automated generation.

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Inspect GitHub PR checks with gh, pull failing GitHub Actions logs, summarize failure context, then create a fix plan and implement after user approval. Use when a user asks to debug or fix failing PR CI/CD checks on GitHub Actions and wants a plan + code changes; for external checks (e.g., Buildkite), only report the details URL and mark them out of scope.

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Master AngularJS to Angular migration, including hybrid apps, component conversion, dependency injection changes, and routing migration.

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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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Use this skill when the user asks about buying or selling a trucking company — valuation drivers (revenue, fleet age, CSA scores, customer concentration), asset purchase vs stock purchase, FMCSA authority transfer, due diligence checklist, common deal structures (cash, earnout, seller-financed), and what changes operationally after acquisition. Reference 49 CFR 365.401 (authority transfer).

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Apply rapport-based elicitation to resistant or semi-cooperative humans and agents. Use when coercive prompting or brittle handoffs damage cooperation. NOT for routine cooperative tasks, pure technical debugging, or already reliable exchanges.

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Interpret and design bounded FIPA communicative-act exchanges using XC00037H semantics while keeping delivery, authority, and external effects separate. NOT for proving delivery, task authorization, or external effect completion.

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Apply rapport-based elicitation to resistant or semi-cooperative humans and agents. Use when coercive prompting or brittle handoffs damage cooperation. NOT for routine cooperative tasks, pure technical debugging, or already reliable exchanges.

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Manage database schema with Drizzle ORM and SQLite migrations. Use when adding tables, modifying columns, creating indexes, or running migrations. Activates for database schema changes, migration generation, and Drizzle query patterns.

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Safe database migration manager for zero-downtime DDL changes and rollback plans. Activate on: database migration, schema change, DDL, rollback plan, zero-downtime migration, Prisma migrate, Drizzle kit, Flyway, column rename, table alter. NOT for: query optimization (use database-optimizer), ORM modeling (use data-pipeline-engineer), backup/restore (use devops-automator).

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