Skills de Claude Code · página 98
Skills individuales de Claude Code extraídas de todos los repositorios del directorio: cada SKILL.md, instalable con un comando, con su definición completa y las señales de confianza del repo.
- specify-meta305
Scaffold, status-check, and manage specification directories. Use when creating a new spec, reading spec status, transitioning between phases, or logging decisions on a spec in .start/specs/.
rsmdt/the-startupInstalar Create and validate product requirements documents (PRD). Use when writing requirements, defining user stories, specifying acceptance criteria, analyzing user needs, or working on requirements.md files in .start/specs/.
rsmdt/the-startupInstalarCreate and validate solution design documents (SDD). Use when designing architecture, defining interfaces, documenting technical decisions, analyzing system components, or working on solution.md files in .start/specs/.
rsmdt/the-startupInstalar- specify305
Create a comprehensive specification from a brief description. Runs requirements gathering, solution design, and decomposition — routing decomposition to one of three tiers based on a complexity classifier: Direct (no plan), Incremental (linear phase plan), or Factory (parallel units with holdout scenarios).
rsmdt/the-startupInstalar - validate305
Validate in any of six modes — spec quality, single-file review, spec-to-implementation drift, constitution rule enforcement, comparison between two artifacts, or sanity-checking your understanding. Use when checking a spec by ID, validating a file by path, detecting drift, enforcing constitution rules, comparing two sources ("$X against $Y"), or asking a freeform validation question.
rsmdt/the-startupInstalar Use when creating new skills, editing existing skills, auditing skill quality, converting skills to markdown conventions, or verifying skills before deployment. Triggers include skill authoring requests, skill review needs, or "the skill doesn't work" complaints.
rsmdt/the-startupInstalar- examples305rsmdt/the-startupInstalar
RICE, MoSCoW, Kano, and value-effort prioritization frameworks with scoring methodologies and decision documentation. Use when prioritizing features, evaluating competing initiatives, creating roadmaps, or making build vs defer decisions.
rsmdt/the-startupInstalarIdentify existing codebase patterns (naming conventions, architectural patterns, testing patterns) to maintain consistency. Use when generating code, reviewing changes, or understanding established practices.
rsmdt/the-startupInstalarUnified codebase discovery across structure navigation, tech-stack detection, and documentation extraction. Use when onboarding to a project, locating implementation paths, identifying frameworks/tooling, or validating docs against code reality.
rsmdt/the-startupInstalarRequirement gathering techniques, stakeholder analysis, user story patterns, and specification validation. Use when clarifying vague requirements, resolving conflicting needs, documenting specifications, or validating requirements with stakeholders.
rsmdt/the-startupInstalarUser research and insight synthesis for interviews, usability testing, personas, journey mapping, and actionable product/design recommendations. Use when planning studies, collecting evidence, synthesizing patterns, or converting findings into prioritized decisions.
rsmdt/the-startupInstalarContext enrichment for agentic AI application development using LangChain, Vercel AI SDK, and assistant-ui. Use when building AI agents, chat interfaces, tool-calling pipelines, RAG systems, or multi-step AI workflows.
rsmdt/the-startupInstalarREST and GraphQL API design patterns, OpenAPI/Swagger specifications, versioning strategies, and authentication patterns. Use when designing APIs, reviewing API contracts, evaluating API technologies, or implementing API endpoints.
rsmdt/the-startupInstalarSystem architecture patterns including monolith, microservices, event-driven, and serverless, with C4 modeling, scalability strategies, and technology selection criteria. Use when designing system architectures, evaluating patterns, or planning scalability.
rsmdt/the-startupInstalarUnified domain and data modeling for business entities, invariants, schema design, aggregate boundaries, and evolution strategy. Use when designing business models, schema changes, bounded contexts, or consistency rules.
rsmdt/the-startupInstalarContext enrichment for frontend UI development using shadcn/ui and Tailwind CSS. Use when building component libraries, implementing UI designs, theming, or working with accessible React components.
rsmdt/the-startupInstalarCreate architectural decision records (ADRs), system documentation, API documentation, and operational runbooks. Use when capturing design decisions, documenting system architecture, creating API references, or writing operational procedures.
rsmdt/the-startupInstalar- testing305
Writing effective tests and running them successfully. Covers layer-specific mocking rules, test design principles, debugging failures, and flaky test management. Use when writing tests, reviewing test quality, or debugging test failures.
rsmdt/the-startupInstalar Unified platform operations guidance for CI/CD pipeline design, deployment strategies, observability, SLI/SLOs, and incident-ready rollouts. Use when building release workflows, production monitoring, or reliability controls.
rsmdt/the-startupInstalarUnified code review skill for correctness, design, readability, security, performance, testability, accessibility, and error-handling conventions. Use when reviewing changes, enforcing quality standards, or identifying technical debt.
rsmdt/the-startupInstalarMeasurement approaches, profiling patterns, bottleneck identification, and optimization guidance. Use when diagnosing performance issues, establishing baselines, identifying bottlenecks, or planning for scale. Always measure before optimizing.
rsmdt/the-startupInstalarVulnerability review, threat modeling, OWASP patterns, and secure coding assessment. Use when reviewing code security, designing secure systems, performing threat analysis, or validating security implementations.
rsmdt/the-startupInstalarGenerate cinematic AI shortfilm prompts (works with Seedance 2.0, Xiaoyunque, Sora, Kling, Jimeng, Veo) using the 5-stage structure from Mx-Shell's Zombie Scavenger. Trigger when the user wants transformation sequences, multi-shot narrative shorts, weapon-charge/combat segments, emotional family/pet/farewell narratives (催泪/亲情/萌宠/离别), or any cinematic video prompt.
jnMetaCode/ai-shortfilm-promptsInstalar- daily-brief303
Operational knowledge for the daily-brief digest pipeline (this project). RSS/API fetchers, pluggable LLM enrichment (default claude CLI on Max; also anthropic/openai/deepseek/minimax API), trading section, HTML rendering, cross-platform scheduler integration (Windows Task Scheduler / macOS launchd / Linux cron). Load when the user asks about running daily / regenerating sections / debugging a failed run / adding or disabling sources / LLM quota / scheduler / why a tab shows wrong data / why a source failed / switching LLM backend. Always prefer the documented npm commands over re-implementing logic. Diagnose by reading logs/daily-*.log first, then logs/llm-calls.jsonl for LLM-side issues.
leiting-eric/DailyBriefInstalar Generate scroll-stopping viral hook video prompts for Seedance 2.0 on Higgsfield. Use whenever the user wants viral content, TikTok hooks, Instagram Reels openers, YouTube Shorts, attention-grabbing video, scroll-stopper, pattern interrupt, or any short-form video designed to maximize retention and views. Triggers on any mention of viral, hook, scroll-stop, retention, views, engagement, short-form, TikTok, Reels, Shorts.
Generate SaaS product launch and software demo video prompts for Seedance 2.0 on Higgsfield. Use whenever the user wants a product launch video, app demo, software walkthrough, feature showcase, startup promo, tech product reveal, or any SaaS/software marketing video. Triggers on SaaS, app, software, product launch, demo, feature, startup, tech, UI, dashboard, landing page video.
Generate personal brand and founder story video prompts for Seedance 2.0 on Higgsfield. Use for authority content, day-in-the-life, founder story, personal brand building, thought leadership, creator content, lifestyle videos, behind-the-scenes, or any video meant to build a personal brand presence. Triggers on personal brand, founder, creator, authority, lifestyle, behind the scenes, day in the life, thought leader.
Generate online course and coaching program promotional video prompts for Seedance 2.0 on Higgsfield. Use for course trailers, coaching ads, educational content promos, masterclass teasers, webinar promotions, or any educational product video. Triggers on course, coaching, masterclass, webinar, tutorial, education, teaching, training, class, program, academy.
Generate faceless content video prompts for Seedance 2.0 on Higgsfield. Use for faceless YouTube channels, TikTok content without showing face, anonymous creator content, narration-driven videos, stock-footage-style AI content, or any video where the creator doesn't appear on camera. Triggers on faceless, no face, anonymous, narration, stock footage, b-roll, background video, voiceover video.
Generate luxury and premium aesthetic video prompts for Seedance 2.0 on Higgsfield. Use for luxury brand content, premium product showcases, high-end lifestyle, minimalist aesthetic, elegant brand videos, or any content requiring sophisticated visual treatment. Triggers on luxury, premium, high-end, elegant, minimalist, sophisticated, exclusive, refined, designer, couture, bespoke.
Generate before-and-after transformation video prompts for Seedance 2.0 on Higgsfield. Use for transformation reveals, glow-ups, makeovers, renovation reveals, fitness transformations, design before-after, business growth visuals, or any content showing dramatic change. Triggers on before after, transformation, reveal, glow up, makeover, renovation, redesign, progress, results.
Generate customer testimonial and social proof video prompts for Seedance 2.0 on Higgsfield. Use for customer stories, case study videos, review showcases, social proof content, success story videos, or any content featuring customer results and experiences. Triggers on testimonial, review, case study, social proof, customer story, success story, results, feedback, client.
Generate AI avatar and digital persona video prompts for Seedance 2.0 on Higgsfield. Use for virtual spokesperson content, digital twin videos, AI presenter clips, avatar-based marketing, virtual influencer content, or any video featuring a digital/AI-generated character as the main subject. Triggers on avatar, digital persona, virtual presenter, AI character, digital twin, virtual influencer, synthetic media, animated spokesperson.
Generate podcast clip visualization video prompts for Seedance 2.0 on Higgsfield. Use for podcast clip videos, audio-to-visual content, audiogram alternatives, podcast highlight reels, interview clip visuals, or any video that transforms audio content into engaging visual format. Triggers on podcast, audio clip, audiogram, interview clip, sound bite, audio visual, podcast video, episode highlight, podcast clip.
把旅行行程做成美观、可离线、手机优先的单文件 HTML(交互地图+每日时间轴+出发前订票提醒)。两种用法——只给目的地和天数让它帮你规划,或丢一份现成计划让它直接出页面。触发:旅行计划可视化、做旅行攻略网页、行程 HTML、travel plan visualization。
zexuanw958-svg/travel-plan-vizInstalarCreate production-quality Android applications following Google's official architecture guidance and NowInAndroid best practices. Use when building Android apps with Kotlin, Jetpack Compose, MVVM architecture, Hilt dependency injection, Room database, or multi-module projects. Triggers on requests to create Android projects, screens, ViewModels, repositories, feature modules, or when asked about Android architecture patterns.
dpconde/claude-android-skillInstalarCreate AI agents with Vizra ADK - includes patterns for customer service, data analysis, and content generation agents
vizra-ai/vizra-adkInstalarTest and evaluate AI agents with automated evaluations, assertions, and LLM-as-a-Judge patterns
vizra-ai/vizra-adkInstalarImplement persistent memory, session context, and vector memory (RAG) for AI agents
vizra-ai/vizra-adkInstalarBuild custom tools for Vizra ADK agents - includes patterns for database, API, file, and email tools
vizra-ai/vizra-adkInstalarOrchestrate complex multi-agent workflows - sequential, parallel, conditional, and loop patterns
vizra-ai/vizra-adkInstalar처리방침·이용약관 자동 생성 스킬 패키지 (v4.0). 호출 시 privacy-kr·privacy-eu·privacy-us·privacy-global 4개 하위 스킬을 번호 메뉴로 제시하고 번호 입력 즉시 해당 스킬 인터뷰로 직행. 한국 PIPA + EU GDPR + US CCPA/CPRA 대응.
kimlawtech/korean-privacy-termsInstalar- privacy-eu294
EU 사용자 대상 서비스용 Privacy Notice·Terms of Service·Consent Modal·Cookie Banner 자동 생성. GDPR (Regulation 2016/679) + ePrivacy Directive + Consumer Rights Directive 2011/83 + Digital Services Act + Digital Content Directive + Unfair Terms Directive 반영. 영문 인터뷰로 진행.
kimlawtech/korean-privacy-termsInstalar 한국+일본 병기 처리방침·이용약관 자동 생성. 한국 본사가 일본 사용자까지 대상으로 서비스할 때 사용. 한국어(PIPA)·일본어(APPI) 두 세트 문서를 동시 생성하고, Footer에 언어·관할 전환 링크 자동 삽입.
kimlawtech/korean-privacy-termsInstalar한국+EU 병기 처리방침·이용약관 자동 생성. 한국 본사가 EU 사용자까지 대상으로 서비스할 때 사용. 한국어(PIPA)·영문(GDPR) 두 세트 문서를 동시 생성하고, Footer에 언어·관할 전환 링크 자동 삽입.
kimlawtech/korean-privacy-termsInstalar- privacy-jp294
日本サービス向け(일본 서비스용) プライバシーポリシー・利用規約・同意モーダル・Cookieバナー 자동 생성. 個人情報保護法(APPI)·消費者契約法·特定商取引法 반영. Next.js 13~16 프로젝트 대상.
kimlawtech/korean-privacy-termsInstalar - privacy-kr294
한국 서비스용 처리방침·이용약관·회원가입 동의 모달·쿠키 배너 자동 생성. 개인정보보호법 §30, 2025.4.21 작성지침, 2026.3 개정법, 공정위 전자상거래 표준약관 10023호 반영. Next.js 13~16 프로젝트 대상.
kimlawtech/korean-privacy-termsInstalar 처리방침·이용약관 자동 생성 진입점. 호출 즉시 6개 하위 스킬(privacy-kr·privacy-eu·privacy-us·privacy-jp·privacy-global·privacy-global-jp)을 번호 메뉴로 제시하고, 번호 입력 즉시 해당 스킬 인터뷰로 직행한다.
kimlawtech/korean-privacy-termsInstalar- privacy-us294
미국 CCPA/CPRA + 주요 주법(VCDPA·CPA·CTDPA·UCPA·ICDPA·KCDPA·RIDPA) 기반 Privacy Policy 자동 생성. 2026.1.1 CPPA 갱신 규정, Sensitive Personal Information, Do Not Sell/Share, ADMT 공개, GPC 브라우저 신호 대응. 캘리포니아 거주자 서비스·100K records 초과 서비스 대상.
kimlawtech/korean-privacy-termsInstalar >
Use when maintaining or optimizing OpenClaw workspace files — AGENTS.md, TOOLS.md, SOUL.md, USER.md, IDENTITY.md, HEARTBEAT.md, BOOT.md, MEMORY.md, and related checklists and memory files. Covers workspace auditing, token budget analysis, new agent workspace setup from scratch, memory distillation, and cross-file consistency reviews.
win4r/openclaw-workspaceInstalar- auditing290
Use when reviewing a bundle-plugin for structural issues, version drift, skill quality, workflow integration, or security risks — before releasing, after changes, or after adding skills. Auto-detects scope (full project vs skill vs workflow)
OdradekAI/bundles-forgeInstalar - authoring290
Use when writing, completing, improving, or adapting SKILL.md and agents/*.md in a bundle-plugin — integrating external skills, filling scaffolded stubs, or rewriting for better triggering and token efficiency
OdradekAI/bundles-forgeInstalar - blueprinting290
Use when planning new bundle-plugins, splitting complex skills, combining skills into bundles, or exploring a vague idea about packaging skills
OdradekAI/bundles-forgeInstalar - optimizing290
Use when optimizing a bundle-plugin or single skill — improving descriptions, reducing tokens, fixing audit findings, restructuring workflows, adding skills to fill gaps, or iterating on user feedback
OdradekAI/bundles-forgeInstalar - releasing290
Use when releasing a bundle-plugin, bumping versions, fixing version drift across manifests, setting up version sync infrastructure, updating CHANGELOG, publishing to marketplaces, or checking release readiness
OdradekAI/bundles-forgeInstalar - scaffolding290
Use when generating project structure for new bundle-plugins, adding or removing platform support (Claude Code, Cursor, Codex, OpenCode, Gemini CLI, OpenClaw), updating platform manifests, or migrating hooks and configuration between platforms
OdradekAI/bundles-forgeInstalar Use when starting any conversation - establishes how to find and use skills in the <project-name> project
OdradekAI/bundles-forgeInstalar- testing290
Use when testing a bundle-plugin locally before release — generating dev-marketplace environments, verifying component discovery, running hook smoke tests, and validating cross-platform readiness
OdradekAI/bundles-forgeInstalar Use when starting any conversation involving bundle-plugins — blueprinting, scaffolding, authoring, auditing, testing, optimizing, or releasing. Also use when feeling unsure which bundles-forge skill applies
OdradekAI/bundles-forgeInstalar- ruff289
Guide for using ruff, the extremely fast Python linter and formatter. Use this
astral-sh/claude-code-pluginsInstalar - ty289
Guide for using ty, the extremely fast Python type checker and language
astral-sh/claude-code-pluginsInstalar - uv289
Guide for using uv, the Python package and project manager. Use this when
astral-sh/claude-code-pluginsInstalar - benchmarks287InterfaceX-co-jp/genshijinInstalar
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InterfaceX-co-jp/genshijinInstalar- genshijin287
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InterfaceX-co-jp/genshijinInstalar - components286ThibautMelen/agentic-ai-systemsInstalar
- runtm286
Runtm (Runtime) Cloud CLI for AI agents. Full cloud-API surface: sessions (CRUD + files + env + deploy + lifecycle + history + events + visibility + collaborators), org templates (CRUD + build + fix-session + snapshot + secrets), activity telemetry, secrets, instructions, guardrails, integrations. Trigger on: runtm, runtime, runtm cloud, runtime cloud, runtm session, runtime session, cloud sandbox.
runtm-ai/runtmInstalar |
jaechang-hits/SciAgent-SkillsInstalarOpentrons Protocol API v2 for OT-2/Flex: Python protocols for pipetting, serial dilutions, PCR, plate replication; control thermocycler, heater-shaker, magnetic, temperature modules. Use pylabrobot for multi-vendor.
jaechang-hits/SciAgent-SkillsInstalarInteractive visualization with Plotly. 40+ chart types (scatter, line, heatmap, 3D, geographic) with hover, zoom, pan. Two APIs: Plotly Express (DataFrame) and Graph Objects (fine control). For static publication figures use matplotlib; for statistical grammar use seaborn.
jaechang-hits/SciAgent-SkillsInstalarStatistical visualization on matplotlib + pandas. Distributions (histplot, kdeplot, violin, box), relational (scatter, line), categorical, regression, correlation heatmaps. Auto aggregation/CIs. Use plotly for interactive; matplotlib for low-level.
jaechang-hits/SciAgent-SkillsInstalarBest practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.
jaechang-hits/SciAgent-SkillsInstalarBayesian modeling with PyMC 5: priors, likelihood, NUTS/ADVI sampling, diagnostics (R-hat, ESS), LOO/WAIC comparison, prediction. Hierarchical, logistic, GP variants; predictive checks.
jaechang-hits/SciAgent-SkillsInstalarTime-to-event modeling with scikit-survival: Cox PH (elastic net), Random Survival Forests, Boosting, SVMs for censored data. C-index, Brier, time-dependent AUC; Kaplan-Meier, Nelson-Aalen, competing risks. Pipeline/GridSearchCV compatible. Use statsmodels for frequentist, pymc for Bayesian, lifelines for parametric.
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jaechang-hits/SciAgent-SkillsInstalarPython statistical modeling: regression (OLS, WLS, GLM), discrete (Logit, Poisson, NegBin), time series (ARIMA, SARIMAX, VAR), with rigorous inference, diagnostics, and hypothesis tests. Use scikit-learn for ML; statistical-analysis for test choice.
jaechang-hits/SciAgent-SkillsInstalarDL cell/nucleus segmentation for fluorescence and brightfield microscopy. Pre-trained models (cyto3, nuclei, tissuenet) and a generalist flow-based algorithm segment cells without retraining. Outputs label masks for morphology and tracking. Use scikit-image watershed for rule-based; Cellpose when DL generalization across staining is needed.
jaechang-hits/SciAgent-SkillsInstalarParse/write FCS (Flow Cytometry) files v2.0-3.1. Events as NumPy, channel metadata, multi-dataset files, CSV/FCS export. Use FlowKit for gating/compensation.
jaechang-hits/SciAgent-SkillsInstalarInteractive viewer for microscopy. Displays 2D/3D/4D arrays as Image, Labels, Points, Shapes, Tracks layers; supports annotation, plugin analysis, headless screenshots. Core visualization for Python bioimage workflows. Use ImageJ/FIJI for macro processing; napari for Python-native interactive visualization and DL segmentation review.
jaechang-hits/SciAgent-SkillsInstalarComputer vision for bio-image preprocessing, feature detection, real-time microscopy. Color conversion, morphology, contour/blob detection, template matching, optical flow on fluorescence/brightfield. 10-100× faster than pure Python via C++. Use scikit-image for scientific morphometry/regionprops; OpenCV for real-time, video, classical feature extraction.
jaechang-hits/SciAgent-SkillsInstalarPython bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib2 exchange, and ImageJ Ops. Automates Fiji headlessly from Python. Use scikit-image for pure Python without Fiji plugins; napari for visualization.
jaechang-hits/SciAgent-SkillsInstalarPython image processing for microscopy and bioimage analysis. Read/write images, filter (Gaussian, median, LoG), segment (thresholding, watershed, active contours), measure region properties, detect features. SciPy/NumPy ecosystem. Use OpenCV for real-time video; CellPose for DL cell segmentation; napari for visualization.
jaechang-hits/SciAgent-SkillsInstalarPython library for single-particle tracking (SPT) in video microscopy via the Crocker-Grier algorithm. Locate particles (fluorescent spots, colloids, vesicles, cells) per frame, link into trajectories, filter short tracks, and compute MSD for diffusion analysis. 2D/3D with subpixel accuracy; reads TIF stacks, AVI, image series via pims. Use for quantitative SPT and diffusion coefficient extraction from fluorescence or brightfield video.
jaechang-hits/SciAgent-SkillsInstalarLow-level Python plotting for scientific figures: publication-quality line, scatter, bar, heatmap, contour, 3D; multi-panel layouts; fine control of every element. PNG/PDF/SVG export. Use seaborn for quick stats, plotly for interactive.
jaechang-hits/SciAgent-SkillsInstalarInteractive scientific visualization with Plotly. Two APIs: plotly.express (px) for one-liner DataFrame plots, plotly.graph_objects (go) for trace-level control. 40+ chart types with hover, zoom, pan, animation. Exports HTML or static PNG/SVG/PDF via kaleido. Use for volcano plots with gene hover, dose-response dashboards, expression heatmaps, 3D molecular views. Use seaborn for stats; matplotlib for publication figures.
jaechang-hits/SciAgent-SkillsInstalarGuide for choosing and creating scientific visualizations for publications and talks. Covers chart-type selection by data structure, color theory for accessibility/print, figure composition, journal formatting (Nature, Cell, ACS), and common pitfalls. Consult when visualizing data or preparing submission figures.
jaechang-hits/SciAgent-SkillsInstalarStatistical visualization on matplotlib with native pandas support. Auto aggregation, CIs, grouping for distributions (histplot, kdeplot), categorical (boxplot, violinplot), relational (scatterplot, lineplot), regression (regplot, lmplot), matrix (heatmap, clustermap), grids (pairplot, FacetGrid). Use for quick statistical summaries; matplotlib for fine control; plotly for interactive HTML.
jaechang-hits/SciAgent-SkillsInstalarGuide for annotating statistical significance (p-value asterisks) on comparison plots. Covers standard notation (ns, *, **, ***, ****), matplotlib bracket+asterisk implementation, and use with seaborn box/violin/bar plots. Use when preparing publication-ready figures with significance markers.
jaechang-hits/SciAgent-SkillsInstalarFast short-read DNA aligner for WGS/WES/ChIP-seq. 2× faster BWA-MEM successor; outputs SAM/BAM with read group headers for GATK. Primary plus supplementary records for chimeric reads. Use STAR for RNA-seq splice-aware alignment; Bowtie2 is a comparable alternative.
jaechang-hits/SciAgent-SkillsInstalarRead/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. Region queries, pileup, variant filtering, read groups. Python htslib wrapper exposing samtools/bcftools CLI. Use STAR/BWA for alignment; GATK/DeepVariant for variant calling.
jaechang-hits/SciAgent-SkillsInstalarCLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge. Required between alignment and variant/peak calling. Use pysam for Python-native BAM access; deeptools for normalized coverage tracks.
jaechang-hits/SciAgent-SkillsInstalarSplice-aware RNA-seq aligner producing sorted BAM and splice junction tables. Builds genome index, runs two-pass alignment for better junctions. Outputs sorted BAM, junctions (SJ.out.tab), stats (Log.final.out), optional gene counts. Use Salmon for fast pseudoalignment; STAR when a BAM is needed for variant calling, IGV, or ENCODE pipelines.
jaechang-hits/SciAgent-SkillsInstalarAnnotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRNA, tRNA, rRNA, tmRNA, sORFs, CRISPR arrays, oriC/oriV/oriT, and gaps against a curated UniRef-derived database. Produces NCBI-compatible GFF3, GenBank, EMBL, JSON, FASTA, TSV, and a circular genome plot. Use Prokka for legacy pipelines or non-bacterial kingdoms; PGAP for NCBI GenBank submission.
jaechang-hits/SciAgent-SkillsInstalar