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概要と使いどころ
JIRA issue CRUD via the jira-as wrapper. Triggers: 'create bug/task/story', 'show me PROJ-123', 'get/view/look up issue', 'update PROJ-123', 'delete PROJ-123'. NOT for transitions (mk:jira-lifecycle); NOT for comments/attachments (mk:jira-collaborate); NOT for bulk ops (mk:jira-bulk); NOT for issue links (mk:jira-relationships); NOT for time logging (mk:jira-time); NOT for sprint/epic (mk:jira-agile).
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Implementing the `Idempotency-Key` HTTP header pattern (Stripe-pioneered, IETF-standardizing) so retries don't double-charge or duplicate side effects — full Postgres schema with recovery-point state machine, fingerprint check, in-progress lock with 409 response, and 24h retention. Grounded in Stripe blog/docs, the IETF httpapi WG draft, and Brandur Leach's canonical implementation.
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State-of-the-art data visualization for React/Next.js/TypeScript with Tailwind CSS. Creates compelling, tested, and accessible visualizations following Tufte principles and NYT Graphics standards. Activate on "data viz", "chart", "graph", "visualization", "dashboard", "plot", "Recharts", "Nivo", "D3". NOT for static images, print graphics, or basic HTML tables.
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Extracts cfDNA fragmentomics features (DELFI genome-wide short/long ratios, WPS nucleosome positioning, Griffin GC-corrected accessibility profiles, end-motifs/MDS, OCF) for cancer detection and tissue-of-origin from plasma WGS. Centers on the nuclease-footprint reframe (every feature re-reads one nucleosome object), the mandatory GC correction, and the cross-protocol non-comparability that breaks naive classifiers. Runs FinaleToolkit (real CLI/Python, MIT) and the Griffin Snakemake pipeline; DELFI is a method, not a package. Use when deriving fragment-based signal from cfDNA, choosing a feature family for detection vs subtyping, or diagnosing why a fragmentomic model failed validation.
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Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for visualisation.
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Build clustered heatmaps for expression matrices and other features-by-samples data with rigorous distance/linkage/scaling choices, robust color mapping, optimal leaf ordering, and ComplexHeatmap/pheatmap/seaborn rendering. Covers the ward.D vs ward.D2 trap, the row-vs-column scaling decision, multi-track annotations, oncoPrint, and raster rendering for large matrices. Use when visualizing expression patterns across samples or identifying co-regulated clusters.
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Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.
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Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.
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Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.
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Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.
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Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correlates with conditions, computing per-sample motif z-scores after matched background correction, comparing to ArchR / Signac equivalents, or distinguishing motif-accessibility signal from per-site footprinting.
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Search arXiv preprint repository for papers in physics, mathematics, computer science, quantitative biology, and related fields
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。
Reconcile baseline-versioned files that the `create-baseline upgrade` CLI staged for LLM-assisted semantic merge. Use when the CLI prints "Open Claude Code and run /upgrade-project to reconcile". Reads the stage manifest at `.claude/state/upgrade/<ts>/manifest.json`, reasons through each pending file's three-way delta in main context, writes a reconciled LOCAL, then deletes the stage when every file lands. Supports `--dry-run` (preview the reconciled diff without writing) and a structured "needs-user-input" fallback when the conflict cannot be disambiguated automatically.
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Run an org-team workflow — a flat pod of up to four peer Claude Code sessions claims lane-tagged slices of an approved spec over the baseline MCP channel and implements them concurrently, each in its own git worktree. Each peer DECIDES its own in-lane implementation choices in its own main context (Article X); only un-decidable or cross-lane forks escalate peer→lead→human (yield_fork for task-bound forks, ask_lead for free-form queries). Opt-in and OFF by default (velocity.org_mode.enabled). Graduates the retired sprint-dispatch prototype into the constitutionally-sanctioned org-team model (Article X — Multi-session coordinated workflows). Requires git.
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Power batch-sprint helper — hosts the two behaviours that distinguish the `power` workflow track from spec-entry. (1) Per-ticket iteration: security runs once PER TICKET over workflow.json.tickets[] while the mechanical phases run once for the batch. (2) Commit split: at the commit phase, group the batch's working tree into ordered Conventional Commits via commit-split.mjs, closure last. Invoked within a `power`-track workflow; not a standalone feature. Opt-in via velocity.power_mode.enabled; requires git.
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Preflight a spec draft without saving. Runs the same checks as the write-boundary hooks — PlantUML syntax, required diagram presence, AC-to-sequence traceability, Design calls quality floor, and System delta row resolution — and prints a compact pass/fail table. Use while iterating so the hooks don't bite on save.
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Find the papers that answer a research query in Firecrawl's research paper index — a corpus of paper abstracts whose largest share is biomedical and life-science literature (PubMed, bioRxiv, medRxiv), alongside arXiv preprints in CS, physics, and math — using semantic search, semantic and structural expansion, and in-body verification. Use this skill for literature-finding and paper-retrieval tasks of any kind, including clinical, biomedical, drug, gene, disease, and other life-science questions, whether the answer is a single paper or a full multi-paper set. The index is reached only through the `firecrawl_research_*` MCP tools or the `firecrawl research` CLI subcommands. Calling `firecrawl_search` with its `categories` option set to `["research"]` is a different feature — it filters ordinary web search to research-affiliated websites (the list includes PubMed, bioRxiv, medRxiv, arXiv, and publisher sites) and returns page results from them, without querying the paper records in this index.
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Use for design thinking, or when a product or service problem needs user understanding before solutions: "what do users really need?", "how might we...", "plan a discovery sprint", "validate this concept". Skip when the spec is frozen or the task is code maintenance.
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。
Control Bambu Lab 3D printers locally via MQTT.
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。
Operate and troubleshoot BambuLab printers with the bambu-cli.
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。
Scrum master for sprint planning and story preparation. Use when the user asks to talk to Bob or requests the scrum master.
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。
Execute story implementation following a context filled story spec file. Use when the user says "dev this story [story file]" or "implement the next story in the sprint plan"
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。
When turning a locked still + blueprint into a provider-tuned motion prompt — camera, primary + secondary motion, physics, native-audio sync. Triggers 'motion prompt for Veo/Kling/Sora'.
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Use when the user wants to learn a topic or verify real understanding — rapid-competence session, error drills, learning sprint, gap probe, Feynman check. Triggers 'teach me X', 'quiz me'.
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。