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Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette.

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The BloodGen3Module package provides functions for R user performing module repertoire analyses and generating fingerprint representations. Functions can perform group comparison or individual sample analysis and visualization by fingerprint grid plot or fingerprint heatmap. Module repertoire analyses typically involve determining the percentage of the constitutive genes for each module that are significantly increased or decreased. As we describe in details;https://www.biorxiv.org/content/10.11

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Generate SuperSigs (supervised mutational signatures) from single nucleotide variants in the cancer genome. Functions included in the package allow the user to learn supervised mutational signatures from their data and apply them to new data. The methodology is based on the one described in Afsari (2021, ELife).

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Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed fu

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Operational playbook for running cold email continuously. Prescribes what to do on Monday / Wednesday / Friday / biweekly / monthly / quarterly. Use this as your ongoing cadence once your first campaign is live. What separates hobbyist from top 1% operators isn't tooling — it's consistency. This skill is the schedule.

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Pulls replies from a Smartlead campaign, classifies each as positive/neutral/negative/OOO/bounce/unsubscribe using Claude, and reports the positive reply rate — the north-star metric for cold email. Use when the user wants to know if a campaign is actually working (not just getting replies, but getting the RIGHT replies). Triggers on "score my replies", "how's campaign X doing", "positive reply rate", "is this campaign working".

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One sentence that describes WHEN to invoke this skill. Write it as a trigger phrase, not a summary — include the words a user would say ("fix bug", "add feature", "review diff"). The agent routes on this field.

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本地录音转文字工具。当用户发送已有录音、音频或视频文件，并希望把语音转成 Markdown 文稿和 SRT 字幕时使用。Apple Silicon 优先用 MLX/Apple GPU 和 whisper-large-v3-turbo-q4，本地转写，不生成 txt/json/vtt，不用于现场临时录音，也不默认调用云端语音识别服务。

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Rewrites scene descriptions using professional cinematography language, structures prompts with a six-slot formula (camera + subject + action + setting + style + lighting), and diagnoses content filter rejections via a preflight linter. Use whenever the user asks for a Seedance 2.0 / Seedance Pro prompt, describes a scene for Seedance generation, mentions Seedance, reports a Seedance generation failure or flagged prompt, or is burning credits on Seedance regenerations.

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Use when the user asks about camera movements, shot types, or how to describe camera behavior in a Higgsfield prompt. Contains all named camera controls with descriptions, best use cases, and example prompt phrases.

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Guides collaborative requirements discovery before implementation. Creates task directory, seeds PRD, asks high-value questions one at a time, researches technical choices, and converges on MVP scope. Use when requirements are unclear, there are multiple valid approaches, or the user describes a new feature or complex task.

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Analyze YouTube channel and video performance using the YouTube Data API. Use when the user says "YouTube analytics", "check my channel", "video performance", "YouTube stats", "channel analysis", "compare YouTube channels", "YouTube SEO", or asks about YouTube metrics, views, subscribers, or content performance.

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Create lead magnets and gated content to capture email subscribers and leads. Use when asked to design checklists, templates, calculators, mini-courses, whitepapers, or other downloadable content offers. Trigger phrases: "lead magnet", "gated content", "email capture", "content offer", "free download", "checklist", "template", "whitepaper", "swipe file", "content upgrade", "opt-in offer".

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Plan and grow an email newsletter. Use when the user says "newsletter strategy", "grow my newsletter", "newsletter content", "email newsletter", "subscriber growth", "newsletter monetization", "Substack strategy", "Beehiiv", or asks about building, growing, or monetizing a newsletter.

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Write an email drip sequence for affiliate marketing. Triggers on: "write me an email sequence", "create a drip campaign", "email nurture sequence", "affiliate email funnel", "welcome email series", "email onboarding sequence", "write emails for my list", "set up a drip sequence", "email campaign for [product]", "nurture my subscribers", "email follow-up sequence", "build my email funnel", "write 5 emails promoting [product]", "email automation sequence".

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Emit .harness/oia-manifest.json declaring layer alignment with the OIA v0.1 9-layer reference architecture. Self-describes the harness's MCP wiring, witness signing, audit log, identity posture (always 'none' at v0.1). --check verifies an existing manifest, --dry-run prints without writing, --json emits to stdout.

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Weekdays. Takes the one card the standup marked next and turns it into a reviewable change on a branch, never a deployment. It reads the project's own rules and docs first, makes the smallest change the card describes, runs that project's own gate, writes a change brief with the rollback in one line, and pushes the branch for the member to merge. It never merges, never deploys, never applies a migration, and never rotates a key.

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Use when a specific campaign needs a brief the whole team can execute from — context, objective, audience, core message, creative direction, channels, deliverables, week-by-week timeline, approval gates, and risks. Trigger on 'campaign brief', 'creative brief', 'launch brief', 'brief the team on this campaign', 'we are running a promo next month', 'what is the plan for this campaign'. Also use when the user describes a promotion out loud and asks for something the team can actually run. Not for — the whole period plan, see `00-marketing-plan-global`; the list of design files needed, see `41-campaign-asset-list-global`; assigning work to one person, see `64-team-brief-global`; a new product launch sequence, see `59-go-to-market-global`.

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Use the HyperFrames CLI development loop: init, add, catalog, capture, lint, check, snapshot, compare, grade-compare, preview, play, present, beats, keyframes, single or batch render, publish, cloud, cloudrun, feedback, lambda, doctor, browser, info, upgrade, skills, compositions, docs, benchmark, telemetry, transcribe, auth, tts, and remove-background. Also use when diagnosing build or render failures. validate, inspect, and layout are deprecated aliases; use check. Covers local, HeyGen-hosted cloud, AWS Lambda, and Google Cloud Run rendering.

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Use for a trivial task the user can describe in one sentence: a typo, config change, small refactor or forgotten commit. Executes inline with no subagents and no PLAN.md; anything needing research or planning belongs to /gsd-quick.

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Speech-to-text transcription via OpenAI Whisper. Supports two modes — Local CLI (no API key, runs on-device) and Cloud API (fast, scalable, requires OPENAI_API_KEY). Use when the user needs to transcribe audio files, translate speech, or convert audio to text.

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Set up, repair, or verify the local AI short-video environment: video-use, FFmpeg, the Source Han Sans TW subtitle font, ElevenLabs credentials, and optional HyperFrames skills. Use whenever a user asks to install, configure, fix, reconnect, or check this editing environment. Do not use for Premiere or CapCut help, or to edit/transcribe media; hand those requests to the editing workflow after setup is verified.

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Edit a user-supplied video into a vertical Reel, Short, TikTok, video diary short, or an approved eight-step AI short-video workflow. Use when the user provides or points to media and asks to transcribe, cut, subtitle, preview, or export a vertical short. Do not use for environment-only setup or generic Premiere Pro or CapCut help.

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Disciplined diagnosis loop for hard bugs and performance regressions. Reproduce → minimise → hypothesise → instrument → fix → regression-test. Use when user says "diagnose this" / "debug this", reports a bug, says something is broken/throwing/failing, or describes a performance regression.

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