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gabrielmoreira

@gabrielmoreira source repo

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• 17 repo stars
• 2 weeks ago last updated

1. ▌
   Syncfusion Maui Signature Pad · gabrielmoreira bundle

   Implements Syncfusion .NET MAUI SignaturePad (SfSignaturePad) for capturing digital signatures with realistic handwritten appearance. Use when working with signature capture, digital signatures, electronic signatures, or signing documents in .NET MAUI applications. Covers stroke customization, saving signatures as images, signature point data retrieval, and signature validation.
   17 repo stars
2. ▌
   Direct Seedance Music Typography · gabrielmoreira bundle

   Plan Seedance 2.0 music-video clips where performance, camera, scene changes, spatial lyric typography, and transitions respond to a locked music window. Use for 4–15 second hooks or longer multi-clip MVs with explicit audio/lyric ownership, subject and scene references, beat-led events, and assembly handoffs; not for ordinary caption cleanup or unlicensed lyric copying.
   17 repo stars
3. ▌
   Hand Bounded Local Medium Window · gabrielmoreira bundle

   Create original short videos using the 手势边界换媒｜局部窗口、多形态验真与回归 Creative DNA for MiniMax H3 or Seedance 2.0. Use when the user wants a hand-defined local medium window, repeated geometry proof, strict clipping, and a controlled return with new subjects and surfaces.
   17 repo stars
4. ▌
   Stage Startle To Truce Encounter · gabrielmoreira bundle

   Design short cinematic encounters that move from calm observation to an impossible close appearance, a readable startle response, and a restrained truce gesture for MiniMax H3 or Seedance 2.0. Use when a user wants fantasy-versus-technology contrast, cockpit or window eyelines, pursuit compressed into 4–15 seconds, non-lethal escalation, identity-reference continuity, or a tense scene that resolves through performance instead of injury or dialogue exposition.
   17 repo stars
5. ▌
   Saas Landing Gen · gabrielmoreira

   Generate a complete SaaS landing page with EdgeOne Pages deployment. Includes hero section, features, pricing, testimonials, and CTA sections. Supports React + Tailwind CSS, one-command deploy to EdgeOne Pages.
   17 repo stars
6. ▌
   Uc Interviewer · gabrielmoreira

   User journey interview, use case interview, 用户旅程访谈。Use when: BRD 完成后需要梳理用户旅程、"对齐 use case"、"确认用户操作流程"。
   17 repo stars
7. ▌
   Godot Adapt Single To Multiplayer · gabrielmoreira bundle

   Expert patterns for adding multiplayer to single-player games including client-server architecture, authoritative server design, MultiplayerSynchronizer, lag compensation (client prediction, server reconciliation), input buffering, and anti-cheat measures. Use when retrofitting multiplayer, porting to online play, or designing networked gameplay. Trigger keywords: MultiplayerPeer, ENetMultiplayerPeer, SceneMultiplayer, MultiplayerSynchronizer, rpc, rpc_id, multiplayer_authority, client_prediction, server_reconciliation, lag_compensation, rollback.
   17 repo stars
8. ▌
   Apm Package Author · gabrielmoreira

   Create, maintain, and troubleshoot APM (Agent Package Manager) manifests for distributing GitHub Copilot skills, agents, and MCP servers. USE FOR: creating apm.yml root manifests; creating packages/* sub-manifests; bundling MCP server config into a package; installing packages from a GitHub repo; troubleshooting APM install errors (missing .vscode/mcp.json, Codex CLI warnings, cached installs). DO NOT USE FOR: general GitHub Copilot customization questions; creating SKILL.md files (use skill-creator); writing MCP server code.
   17 repo stars
9. ▌
   Trading212 API · gabrielmoreira

   This skill should be used when the user asks to "connect to Trading 212", "authenticate Trading 212 API", "place a trade", "buy stock", "sell shares", "place market order",, "place pending order", "place limit order", "cancel order", "check my balance", "view account summary", "get positions", "view portfolio", "check P&L", "find ticker symbol", "search instruments", "check trading hours", "view dividends", "get order history", "export transactions", "generate CSV report", or needs guidance on Trading 212 API authentication, order placement, position monitoring, account information, instrument lookup, or historical data retrieval.
   17 repo stars
10. ▌
    Differential Review · gabrielmoreira bundle

    Performs security-focused differential review of code changes. Adapts analysis depth to codebase size, uses git blame for context, calculates blast radius by counting callers, checks test coverage of modified code, and generates a markdown report. Use when reviewing a PR, commit, or diff for security vulnerabilities, checking whether a change re-introduces a previously fixed bug, asking what else a change could break, or finding which modified code has no test covering it.
    17 repo stars
11. ▌
    Harness Writing · gabrielmoreira

    Designs and improves fuzzing harnesses for C/C++ and Rust. Covers mapping raw bytes onto a target API, generating structured inputs, avoiding non-determinism and false crashes, and deciding what to fuzz together. Use when writing a first LLVMFuzzerTestOneInput or fuzz_target! harness, when a campaign finds nothing or reports crashes that will not reproduce, or when the target API needs structured rather than raw input.
    17 repo stars
12. ▌
    Writing Lean Proofs · gabrielmoreira

    Writes and reviews structured Lean 4 proofs and designs Lean libraries following Mathlib conventions. Use when proving theorems in Lean, formalizing mathematics or specifications in Lean 4, defining new types or definitions in a Lean library, reviewing Lean proofs for readability and maintainability, refactoring long tactic proofs into lemmas, filling in sorry placeholders in a Lean development, setting up CI or linters for a Lean project, diagnosing slow proofs or maxHeartbeats timeouts, or writing custom tactics, macros, or linters.
    17 repo stars
13. ▌
    Audience Fit Check · gabrielmoreira bundle

    When the user wants to vet a specific creator's audience fit and brand-safety before working with them. Also use on "is this influencer a good fit," "vet this creator," "brand safety check," "does their audience match," "should we work with [handle]," "creator due diligence," "check this KOL before outreach," or "is this account safe to sponsor." Reads public posts and engagement only. Read-only research, not outreach.
    17 repo stars
14. ▌
    Social Listening Brief · gabrielmoreira bundle

    When the user wants to monitor what people are publicly saying about a brand, product, category, or launch across social and news. Also use on "social listening," "brand monitoring," "what are people saying about us," "monitor mentions," "track our launch," "buzz check," "social media monitoring," "are people talking about X," "sentiment on Reddit/X/TikTok," or "what's the chatter." Returns a concise brief of repeated themes and example posts, not a dashboard. Reads public posts only — never posts, replies, or DMs. For deep subreddit mapping, see reddit-community-research.
    17 repo stars
15. ▌
    Agents Hooks · gabrielmoreira

    Configures Claude Code hooks and Codex hooks.json/notify callbacks. Use when adding guardrails, preflight, audit trails, worktree automation, or budget enforcement.
    17 repo stars
16. ▌
    Document PDF · gabrielmoreira

    Extracts, creates, and transforms PDF documents. Use when parsing text or tables, generating files, merging pages, or handling PDF forms.
    17 repo stars
17. ▌
    QA Debugging · gabrielmoreira

    Systematic debugging for crashes, regressions, flakes, and production bugs. Use when diagnosing stack traces, logs, traces, or profiling data.
    17 repo stars
18. ▌
    Research Git · gabrielmoreira

    Scans public GitHub repos for agent skills, dev practices, and code patterns. Use when enriching skills, setting team policy, or researching a build domain.
    17 repo stars
19. ▌
    Auto Review Loop LLM · gabrielmoreira

    Autonomous research review loop using any OpenAI-compatible LLM API. Configure via llm-chat MCP server or environment variables. Trigger with "auto review loop llm" or "llm review".
    17 repo stars
20. ▌
    Idea Discovery Robot · gabrielmoreira

    Workflow 1 adaptation for robotics and embodied AI. Orchestrates robotics-aware literature survey, idea generation, novelty check, and critical review to go from a broad robotics direction to benchmark-grounded, simulation-first ideas. Use when user says "robotics idea discovery", "机器人找idea", "embodied AI idea", "机器人方向探索", "sim2real 选题", or wants ideas for manipulation, locomotion, navigation, drones, humanoids, or general robot learning.
    17 repo stars
21. ▌
    Interview Cheatsheet · gabrielmoreira

    Generate a long-form Chinese interview-prep cheat sheet on a specific ML/LLM topic — formulas with derivations, from-scratch PyTorch code, comparison tables, and 25 高频面试题 (L1 必会 / L2 进阶 / L3 顶级 lab). Use when the user says '写面试 cheat sheet', '写一份 X 教程', '帮我准备 Y 面试题', '出一份 X 速查', or wants a 600-1000 line Chinese tutorial on a specific ML topic.
    17 repo stars
22. ▌
    Patent Novelty Check · gabrielmoreira

    Assess patent novelty and non-obviousness against prior art. Use when user says "专利查新", "patent novelty", "可专利性评估", "patentability check", or wants to evaluate if an invention is patentable.
    17 repo stars
23. ▌
    Paper To Agent Guide · gabrielmoreira

    Transform research papers into interactive AI agents for exploration
    17 repo stars
24. ▌
    Obsidian Citation Guide · gabrielmoreira

    Citation plugin for Obsidian note-taking with BibTeX support
    17 repo stars
25. ▌
    Latex Templates Collection · gabrielmoreira

    Collection of LaTeX templates for papers, presentations, and CVs
    17 repo stars
26. ▌
    Developer Mentor · gabrielmoreira

    Guide users through software development concepts, decisions, and problem-solving without writing or implementing code. Use when a user asks for help understanding a concept, wants guidance on architecture or design decisions, needs help debugging their thinking, wants to learn best practices, or seeks mentorship on how to approach a development task. Covers concept explanation, design guidance, debugging mentorship, code review teaching, and learning path recommendations.
    17 repo stars
27. ▌
    Threat Modelling · gabrielmoreira

    Analyse repositories and deployed cloud infrastructure to produce STRIDE-based threat model documents with Mermaid architecture diagrams, prioritised threats, and recommendations. Use when a user asks to create a threat model, identify threats, assess attack surfaces, review an existing threat model, or update a threat model after system changes.
    17 repo stars
28. ▌
    On Call Handoff Patterns · gabrielmoreira

    Master on-call shift handoffs with context transfer, escalation procedures, and documentation. Use this skill when transitioning on-call responsibilities between engineers and ensuring the incoming responder has full situational awareness, when writing a shift summary that captures active incidents, ongoing investigations, and recent changes, when handing off mid-incident so a fresh engineer can take over the incident commander role without losing context, when onboarding a new engineer to the on-call rotation for the first time, or when auditing and improving the quality of existing handoff processes across teams.
    17 repo stars
29. ▌
    Langchain Architecture · gabrielmoreira

    Design LLM applications using LangChain 1.x and LangGraph for agents, memory, and tool integration. Use when building LangChain applications, implementing AI agents, or creating complex LLM workflows.
    17 repo stars
30. ▌
    Finetuning Method Selection · gabrielmoreira

    Decide whether to fine-tune at all, and route to the right method (SFT, DPO/ORPO/KTO, GRPO/RLVR, continued pretraining) and base model. Use when starting any fine-tuning effort, when unsure whether RAG or prompting would suffice, or when choosing between preference-optimization and reinforcement methods.
    17 repo stars
31. ▌
    Send Experiment Designer · gabrielmoreira

    Use when the user asks to "design an email A/B test", "set up a multivariate subject/CTA test", "run a send-time test", "build a hold-out group", or "is this email result statistically and practically material?"; produces a falsifiable hypothesis, one-variable-per-cell matrix, sample-size/MDE/duration/power plan, and an effect/uncertainty read from own ESP data. Applies only a precommitted owner-approved action rule; the helper never chooses a business action. Not for EQS/vetoes or writing the email. 邮件AB测试设计/多变量测试/发送时间测试/留出组/显著性判定
    17 repo stars
32. ▌
    Performance Analyzer · gabrielmoreira

    Use when the user asks to "analyze influencer campaign performance", "compare influencers", or "find what content worked"; produces metric scorecards vs target and benchmark, platform/influencer/content rankings, engagement-quality and sentiment reads, conversion-attribution breakdowns, and ranked learnings. Not for dollar-level return math — use roi-calculator. 达人营销效果分析/投放复盘
    17 repo stars
33. ▌
    Story Bank Builder · gabrielmoreira

    Use when the user asks to "build a story bank", "collect our origin and customer stories", or "assemble reusable proof stories for the message"; assembles reusable narrative units — origin, founder, customer, transformation, and proof stories — each tagged to a claims-ledger ID and a message-house pillar, with every proof labeled Measured / User-provided / [needs source]. Not for authoring the message house or pillars — use message-system-architect; not for brand voice or naming rules — use brand-language-codifier; not for finished long-form prose — use content-writer; not for adjudicating whether a proof is true — use offer-claims-registry. 品牌故事库/起源客户转化/证据故事单元
    17 repo stars
34. ▌
    Pitch Narrative Builder · gabrielmoreira

    Use when the user asks to "build our pitch deck narrative", "write a fundraising story", or "structure the sales pitch narrative"; derives from the narrative canon a company pitch/deck narrative — problem → the undeniable shift → product-as-hero → proof → the ask — as a slide-beat outline (one narrative beat per slide, with the claim ID each proof beat rests on), for both a sales pitch and a fundraising deck. Every proof beat is labeled Measured / User-provided / '[needs source]' and unverified ones route to the claims candidates. Not for the launch-window battle cards and talk track — use sales-enablement-kit; not for the durable message hierarchy or the arc itself — use message-system-architect / strategic-narrative-designer; not for finished deck visual design — out of scope; not for claim adjudication — use offer-claims-registry. 路演叙事/融资故事/销售 pitch/幻灯节拍
    17 repo stars
35. ▌
    Audience Belief Mapper · gabrielmoreira

    Use when the user asks to "map what our buyers believe", "capture the objections we keep hearing", or "find the switching forces that move the beachhead"; produces a belief map of the beachhead — held beliefs and mental models, the recurring objections and their reframes, and the JTBD four forces (push of the problem, pull of the new, anxiety of switching, habit of the present) — each item sourced from interviews or win-loss notes (User-provided) and labeled Measured / User-provided / Estimated, with any unverified quote or comparative claim marked "[needs source]" and routed to the claims candidates, never adjudicated here. Not for demographic or persona profiling — use audience-mapper; not for the positioning canvas — use positioning-truth-tracer. 受众信念/异议地图/切换四力/流失语言
    17 repo stars
36. ▌
    Advocacy Program Designer · gabrielmoreira

    Use when the user asks to "design an employee advocacy program", "set up founder-led sharing", or "build a share kit for the team"; produces an advocacy program blueprint in two modes — participation-driven opt-in (default) or top-down assigned with its coercion and authenticity risks flagged — with a voluntary opt-in roster spec submitted as channel-registry proposal events, share kits with mandatory per-person variation, staggered human posting windows plus anti-pod guardrails (no coordinated identical reshares, no engagement rings), per-person material-connection disclosure lines per FTC and 《互联网广告管理办法》, and a Slack/Teams distribution spec. Not for paid creator campaigns — use campaign-planner. 员工倡导/创始人IP分享/内部分享计划/披露合规
    17 repo stars
37. ▌
    Social Measurement Loop · gabrielmoreira

    Use when the user asks to "run the weekly social readout", "which denominator does our engagement rate use", or "which posts won this week and what changes next cycle"; produces the organic-social metric dictionary (every rate names its denominator — ERR engagement-by-reach vs ERI by-impressions vs ER-by-follower — locked across periods), median-not-mean per-post rollups with organic and boosted separated, EMV as labeled exec-translation only (never inside any score), an attributed CHAOSS/Orbit-style community-health readout with employees excluded, and the best/worst-performer write-back the next calendar cycle consumes. Not for dollar-ROI math or the ECHO profile result gate verdict — use roi-calculator and social-quality-auditor. 社媒周报/互动率分母/指标字典/复盘回写
    17 repo stars
38. ▌
    Anti Defensive Writing En · gabrielmoreira

    Stops defensive writing across the entire paper lifecycle — writing, revising, cutting, and organizing experiments. Treats the paper as a press conference, not a project summary, lab log, or self-audit: identify the single most publishable strength of the work and build the most favorable, complete, and persuasive narrative around it. Never present everything evenly, never volunteer weakness, never write an experiment diary, never attack the paper on the reviewer's behalf. Triggers: polish my paper, revise manuscript, write abstract, write introduction, write conclusion, shorten paper, rebuttal, respond to reviewers, organize experiments, defensive writing, AI-flavored academic writing.
    17 repo stars
39. ▌
    Host Computer Use Windows · gabrielmoreira

    Backend-specific Windows guidance for `computer_use_remote`. Load after `status` or `start_session` reports backend_family/backend_id `windows` or Windows UI Automation features. Covers UIA structural targeting, Windows session caveats, and screenshot verification.
    17 repo stars
40. ▌
    Commands Create Slash Command · gabrielmoreira

    Create or update Agent Zero slash commands for the built-in Commands plugin. Use when the user asks to add, edit, duplicate, or refine a reusable /command backed by YAML config plus text/python content files.
    17 repo stars
41. ▌
    Hgnc API · gabrielmoreira

    Access the HGNC (HUGO Gene Nomenclature Committee) database to search for and retrieve gene information including symbols, names, IDs, and other metadata.
    17 repo stars
42. ▌
    Chart Style Unifier · gabrielmoreira

    Batch-unify typography (font family, size, italics) for Word table cells and embedded charts; use when you need consistent formatting across theses/reports without changing body text.
    17 repo stars
43. ▌
    Journal Recommender · gabrielmoreira

    Recommend academic journals based on manuscript topic, abstract, and impact factor expectations. Use when the user wants to find suitable journals for their research manuscript, especially when they provide a topic, abstract, and target Impact Factor.
    17 repo stars
44. ▌
    Meta Search Builder · gabrielmoreira

    Medical literature search strategy generator. Given a user's natural-language description (e.g., meta-analysis topic, PICOS elements, research question), automatically extract medical entities (disease, intervention, population, outcomes) and generate professional search queries for seven major databases (PubMed, Cochrane, Embase, Web of Science, CNKI, Wanfang, VIP). Useful for developing search strategies for systematic reviews and meta-analyses.
    17 repo stars
45. ▌
    Schedule Management · gabrielmoreira

    Local schedule management for adding events, tracking deadlines, generating reminders, and detecting time conflicts when users need offline scheduling with optional popup notifications.
    17 repo stars
46. ▌
    Soft Article Writer · gabrielmoreira

    Generates high-quality promotional soft articles with structured outlines, tailored introductions, and optimized titles based on product info and hot topics. Use when you need to write promotional content, "soft articles" (), or marketing copy that integrates product highlights with current trends, news, or industry insights.
    17 repo stars
47. ▌
    Artifact Design · gabrielmoreira

    Design guidance and fundamentals for Artifacts.
    17 repo stars
48. ▌
    Seedance 2 5 Skill · gabrielmoreira bundle

    Plan and generate controllable Seedance video using Seedream 5.0 Pro storyboards and Seedance 2.0 today, with a Seedance 2.5 route when available. Use for consistent people, products, objects, food, or scenes; storyboard-to- video; reference-to-video; first-and-last-frame image-to-video; extensions; and Atlas Cloud media generation.
    17 repo stars
49. ▌
    Audio Transcribe · gabrielmoreira

    Transcribe speech from audio files (mp3, m4a, wav, ogg, flac, webm) to text using the local `whisper` CLI — no API key. Use whenever a task hinges on the spoken content of an audio attachment.
    17 repo stars
50. ▌
    Hyperpod Version Checker · gabrielmoreira

    Check and compare software component versions on SageMaker HyperPod cluster nodes - NVIDIA drivers, CUDA toolkit, cuDNN, NCCL, EFA, AWS OFI NCCL, GDRCopy, MPI, Neuron SDK (Trainium/Inferentia), Python, and PyTorch. Use when checking component versions, verifying CUDA/driver compatibility, detecting version mismatches across nodes, planning upgrades, documenting cluster configuration, or troubleshooting version-related issues on HyperPod. Triggers on requests about versions, compatibility, component checks, or upgrade planning for HyperPod clusters.
    17 repo stars
51. ▌
    Access Review · gabrielmoreira

    Conduct periodic access reviews and certifications. Implement access governance and recertification workflows. Use when managing access compliance.
    17 repo stars
52. ▌
    AI Pipeline Orchestration · gabrielmoreira

    Orchestrate AI/ML pipelines for data ingestion, model training, batch inference, and RAG indexing using Prefect, Airflow, or Dagster. Build reliable, observable, and retriable workflows for production AI systems.
    17 repo stars
53. ▌
    Model Registry Governance · gabrielmoreira

    Establish model registry standards, governance controls, metadata schemas, approvals, and lifecycle policies for enterprise AI deployments.
    17 repo stars
54. ▌
    Sre Dashboards · gabrielmoreira

    Design and operationalize SRE dashboards that surface reliability, latency, error, saturation, and capacity signals across services. Use when building observability views for SLOs, incident response, and executive reliability reporting.
    17 repo stars
55. ▌
    Kubernetes Ops · gabrielmoreira

    Deploy, scale, and manage Kubernetes workloads. Create deployments, services, and configurations, manage cluster resources, troubleshoot pods, and implement production-ready Kubernetes patterns. Use when working with Kubernetes clusters, K8s deployments, or container orchestration.
    17 repo stars
56. ▌
    Vllm Server · gabrielmoreira

    Deploy and manage vLLM for high-throughput LLM inference. Configure continuous batching, tensor parallelism, quantization, and OpenAI-compatible API endpoints for production LLM serving.
    17 repo stars
57. ▌
    Cdn Setup · gabrielmoreira

    Configure CDNs for content delivery. Set up CloudFront, Cloudflare, and Fastly. Use when optimizing global content delivery.
    17 repo stars
58. ▌
    Ssl Tls Management · gabrielmoreira

    Manage SSL/TLS certificates with Let's Encrypt and internal PKI. Configure secure HTTPS, certificate renewal, and cipher suites. Use when implementing secure communications.
    17 repo stars
59. ▌
    Sbom Supply Chain · gabrielmoreira

    Generate, sign, and verify SBOMs and provenance attestations to secure the software supply chain. Use when implementing SLSA controls, artifact trust policies, or compliance evidence for releases.
    17 repo stars
60. ▌
    GCP Secret Manager · gabrielmoreira

    Secure secrets in Google Cloud Secret Manager. Configure IAM policies, integrate with GKE, and manage secret versions. Use when managing secrets in GCP environments.
    17 repo stars
61. ▌
    Unity Manual Material · gabrielmoreira

    Manually create and edit Materials and assign them to objects using Unity Editor UI. For one-off material tweaks that do not need REST automation.
    17 repo stars
62. ▌
    Unity Scene Contracts · gabrielmoreira

    Advise on Unity scene composition contracts
    17 repo stars
63. ▌
    Unity Yooasset Design · gabrielmoreira bundle

    Source-anchored design rules for YooAsset v2.3.18
    17 repo stars
64. ▌
    Hi C 3d Genomics · gabrielmoreira bundle

    Workflow for Hi-C and related 3D genomics analyses including compartments, loops, TADs, differential contacts, and visualization.
    17 repo stars
65. ▌
    Pathway Analysis · gabrielmoreira bundle

    Workflow for enrichment testing, ranked-gene analysis, pathway scoring, and pathway-focused visualization across omics outputs.
    17 repo stars
66. ▌
    Bio Alignment Indexing · gabrielmoreira bundle

    Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
    17 repo stars
67. ▌
    Bio Alignment Trimming · gabrielmoreira bundle

    Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.
    17 repo stars
68. ▌
    Bio Genome Assembly Assembly Polishing · gabrielmoreira bundle

    Polish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka). Essential for improving long-read assembly accuracy. Use when improving assembly accuracy with polishing tools.
    17 repo stars
69. ▌
    Bio Crispr Screens Bagel Essentiality · gabrielmoreira bundle

    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.
    17 repo stars
70. ▌
    Bio Phylo Bayesian Inference · gabrielmoreira bundle

    Run Bayesian phylogenetic analysis with MrBayes, BEAST2, RevBayes, and PhyloBayes including MCMC convergence diagnostics and model comparison. Use when needing posterior probability support, Bayesian model averaging, site-heterogeneous models for deep phylogenies, or formal model comparison via stepping-stone sampling.
    17 repo stars
71. ▌
    Bio Workflows Biomarker Pipeline · gabrielmoreira bundle

    End-to-end biomarker discovery workflow from expression data to validated biomarker panels. Covers feature selection with Boruta/LASSO, classifier training with nested CV, and SHAP interpretation. Use when building and validating diagnostic or prognostic biomarker signatures from omics data.
    17 repo stars
72. ▌
    Bio Single Cell Cell Communication · gabrielmoreira bundle

    Infer cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor interaction analysis. Use when inferring ligand-receptor interactions between cell types.
    17 repo stars
73. ▌
    Bio Chipseq Chip Deep Learning · gabrielmoreira bundle

    Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2025 Nat Genet; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.
    17 repo stars
74. ▌
    Bio Clip Seq Clip Deep Learning · gabrielmoreira bundle

    Predict RBP binding from RNA sequence using deep learning models (RBPNet sequence-to-signal, RNAProt RNN, GraphProt2 GCN with structure, DeepCLIP, DeepRiPe multi-modal CNN) for variant-effect prediction, in silico binding-site discovery, model interpretation, and transfer learning from CLIP and RBNS datasets. Use when computational prediction of RBP binding from sequence is needed, evaluating variant effects on binding without further wet-lab experiments, comparing model performance, or training a custom model on ENCODE eCLIP data.
    17 repo stars
75. ▌
    Bio Clip Seq Clip Preprocessing · gabrielmoreira bundle

    Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.
    17 repo stars
76. ▌
    Bio Crispr Screens Crispresso Editing · gabrielmoreira bundle

    Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.
    17 repo stars
77. ▌
    Bio Multi Omics Data Harmonization · gabrielmoreira bundle

    Preprocessing and harmonization of multi-omics data before integration. Covers normalization, batch correction, feature alignment, and missing value handling across data types. Use when preparing multi-omics datasets for integration analysis.
    17 repo stars
78. ▌
    Bio Atac Seq Deep Learning Atac · gabrielmoreira bundle

    Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or EnFormer. Use when correcting Tn5 bias with neural networks beyond k-mer models, predicting per-base accessibility profiles, scoring in silico variant effects at GWAS or rare-variant SNPs, discovering motifs via DeepLIFT/TF-MoDISco from a trained model, or generating cell-type-specific accessibility predictions for unobserved cell states.
    17 repo stars
79. ▌
    Bio Small Rna Seq Differential Mirna · gabrielmoreira bundle

    Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific considerations. Use when identifying miRNAs that change between treatment groups, disease states, or developmental stages.
    17 repo stars
80. ▌
    Bio Data Visualization Distribution Plots · gabrielmoreira bundle

    Plot per-group distributions of continuous data using boxplots, violins, beeswarms, quasirandom jitter, and raincloud plots with sample-size honesty (Weissgerber 2015), KDE-bandwidth awareness, and N-aware encoding choices. Use when comparing distributions across a small number of groups — expression per cluster, biomarker per arm, scores per condition — and the bar-of-mean default is misleading.
    17 repo stars
81. ▌
    Bio Crispr Screens Drugz Chemogenomic · gabrielmoreira bundle

    Analyzes CRISPR drug-modifier (chemogenomic) screens with drugZ (Li & Hart 2019 Genome Med), a bidirectional Z-score method that identifies synthetic-lethal sensitizing genes and resistance-conferring suppressor genes from vehicle vs drug comparisons. Covers vehicle-anchored design (not Day-0), the bidirectional Z math giving 2-3x sensitivity over MAGeCK / STARS / edgeR / RIGER on drug screens, per-gene sumZ and normZ, synth (sensitizer) vs supp (suppressor) FDR, multi-dose handling, integration with control sgRNAs, and comparison with MAGeCK MLE with dose covariate. Use when running a drug-modifier CRISPR screen, identifying sensitizing or resistance genes for a drug candidate, choosing drugZ vs MAGeCK MLE for chemogenomic analysis, troubleshooting low-effect drug screens where MAGeCK lacks sensitivity, or designing a drug-screen layout (vehicle vs drug arms).
    17 repo stars
82. ▌
    Bio Duplicate Handling · gabrielmoreira bundle

    Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.
    17 repo stars
83. ▌
    Bio Clinical Databases Gnomad Frequencies · gabrielmoreira bundle

    Queries gnomAD v4 (807k samples), v3, v2.1.1, and constraint metrics with grpmax FAF95, bottleneck-group exclusion, LOEUF interpretation, SV/CNV/mtDNA catalogs, and Whiffin max-credible-AF framework. Use when filtering rare variants, applying ACMG BS1/BA1, ranking genes by LoF intolerance, or selecting between v2 (GRCh37 + chrX/Y constraint) and v4 (GRCh38 + 807k samples).
    17 repo stars
84. ▌
    Bio Genome Assembly Long Read Assembly · gabrielmoreira bundle

    De novo genome assembly from Oxford Nanopore or PacBio long reads using Flye and Canu. Produces highly contiguous assemblies suitable for complete bacterial genomes and resolving complex regions. Use when assembling genomes from ONT or PacBio reads.
    17 repo stars
85. ▌
    Bio Causal Genomics Mediation Analysis · gabrielmoreira bundle

    Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or double-ML medDML. Use when testing whether a molecular phenotype (expression, methylation, protein) mediates a treatment-outcome relationship, decomposing exposure-mediator interaction via VanderWeele 4-way, screening high-dimensional EWAS mediators, or running MR-based mediation when sequential ignorability is implausible.
    17 repo stars
86. ▌
    Bio Methylation Methylkit · gabrielmoreira bundle

    DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons. Use when analyzing single-base methylation patterns, comparing samples, or preparing data for DMR detection.
    17 repo stars
87. ▌
    Bio Data Visualization Multipanel Figures · gabrielmoreira bundle

    Compose multi-panel publication figures with patchwork, cowplot, gridExtra (R), or matplotlib GridSpec/subfigures (Python) including shared axes/legends/guides collection, panel labels in Nature/Cell convention, and journal-spec sizing. Covers patchwork ≥1.2.0 axes='collect' feature, Type-42 font embedding, and the cairo_pdf save path. Use when composing 2+ subpanels into a single figure for journal submission.
    17 repo stars
88. ▌
    Bio Alignment Multiple · gabrielmoreira bundle

    Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.
    17 repo stars
89. ▌
    Bio Comparative Genomics Ortholog Inference · gabrielmoreira bundle

    Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.
    17 repo stars
90. ▌
    Bio Alignment Pairwise · gabrielmoreira bundle

    Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.
    17 repo stars
91. ▌
    Bio Comparative Genomics Pangenome Analysis · gabrielmoreira bundle

    Build and analyze pangenomes for prokaryotes (Panaroo, PPanGGOLiN, PEPPAN, GET_HOMOLOGUES, anvi'o pangenomics) and eukaryotes (Minigraph-Cactus, PGGB, vg pangenome graphs). Implement Tettelin core/accessory/cloud genome decomposition (Tettelin 2005), Heap's law open/closed pangenome modeling, gene presence/absence GWAS (Scoary, pyseer), pangenome graph variant calling (vg, PanGenie), and structural-variation graph indexing. Use when assembling species- or genus-level pan-gene catalogs, separating core from accessory/shell/cloud genes, testing gene-content associations with phenotypes, building pangenome graphs from haplotype-resolved assemblies, calling SVs from pangenome graphs, or selecting between bacterial-pangenome and eukaryotic-pangenome workflows.
    17 repo stars
92. ▌
    Bio Comparative Genomics Positive Selection · gabrielmoreira bundle

    Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.
    17 repo stars
93. ▌
    Bio Reverse Complement · gabrielmoreira bundle

    Generate reverse complements and complements of DNA/RNA sequences using Biopython. Use when working with opposite strands, primer design, or converting between template and coding strands.
    17 repo stars
94. ▌
    Bio Clinical Databases Somatic Signatures · gabrielmoreira bundle

    Extracts and assigns COSMIC v3.4 mutational signatures (84 SBS / 11 DBS / 18 ID / 24 CN / 16 SV) from somatic VCFs using SigProfilerSuite, MutationalPatterns, MuSiCal mvNMF, SigNet, or HRDetect. Use when characterizing DNA-damage etiology (BRCA1/2 HRD, MMR-D, POLE, APOBEC3A, UV, tobacco, aflatoxin, 5-FU/SBS17b, platinum, colibactin SBS88), routing PARP inhibitor decisions, or auditing de novo extraction vs refit choice for cohort size.
    17 repo stars
95. ▌
    Bio Spatial Transcriptomics Spatial Multiomics · gabrielmoreira bundle

    Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.
    17 repo stars
96. ▌
    Bio Spatial Transcriptomics Spatial Proteomics · gabrielmoreira bundle

    Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization. Use when working with multiplexed imaging data, analyzing protein spatial patterns, or integrating spatial proteomics with transcriptomics.
    17 repo stars
97. ▌
    Bio Phylo Tree Visualization · gabrielmoreira bundle

    Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib and modern alternatives. Use when creating tree figures, customizing colors and labels, exporting to image formats, or choosing between Bio.Phylo, ggtree, ETE4, and iTOL for publication.
    17 repo stars
98. ▌
    Bio Variant Annotation · gabrielmoreira bundle

    Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance with MANE transcript selection and pathogenicity scoring. Use when annotating variants with functional and clinical information.
    17 repo stars
99. ▌
    Dependency Planner · gabrielmoreira

    Use this skill whenever a NeuroClaw skill, model, or sub-agent reports a missing dependency (e.g. ImportError, ModuleNotFoundError, command not found), or when the user explicitly requests to install, setup, configure, or fix any library, package, compiler, CUDA toolkit, conda environment, system tool, or git-based repository. Triggers include: 'install', 'setup', 'missing dependency', 'fix import error', 'install torch cuda', 'conda create environment', 'pip install from git', 'install nnU-Net', 'setup gcc nvcc', 'prepare environment for deep learning', 'handle dep error', or any phrase indicating the need to prepare or install software components. This skill is the **mandatory gatekeeper**: it ALWAYS plans first, never installs anything without explicit user confirmation.
    17 repo stars
100. ▌
     Docker Env Manager · gabrielmoreira

     Use this skill whenever the user wants to pull, run, build, compose, list, prune, manage, or otherwise handle Docker containers, images, volumes, networks, or Docker Compose projects, or when a NeuroClaw skill (e.g. wmh-segmentation, freesurfer-processor in container mode) requires a clean, isolated, GPU-enabled Docker environment (e.g. 'pull mars-wmh image', 'run container with GPU', 'docker compose up', 'prune unused images', 'build custom dockerfile', 'manage nvidia docker'). Triggers include: 'docker run', 'docker pull', 'docker compose', 'docker build', 'docker env', 'manage container', 'nvidia docker', 'pull image', 'docker prune', 'containerize'. This skill is the **mandatory gatekeeper for all Docker operations** in NeuroClaw: it ALWAYS plans first, shows commands + risks + best practices, and waits for explicit user confirmation before executing anything. All actual Docker execution is routed through `claw-shell`.
     17 repo stars