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• alibaba-security-center-hardeningHarden Alibaba Cloud security posture via Security Center (threat detection, vulnerability scanning, baseline
• alibaba-serverless-production-readinessReview Function Compute 3.0 (FC3), SAE (Serverless App Engine), and EDAS for production readiness — cold start
• alibaba-solution-architectDesign Alibaba Cloud solutions — product selection (PolarDB vs RDS, ACK vs ASK vs SAE, MaxCompute vs AnalyticD
• alibaba-support-incident-coordinatorCoordinate Alibaba Cloud support incidents — case creation with correct severity (紧急/高/中/低), Enterprise Suppor
• alibaba-ticket-triage-escalation-coordinatorTriage Alibaba Cloud operational alerts, incidents, and support tickets — P0/P1/P2/P3 classification, Alibaba
• alibaba-waf-cost-optimization-reviewAssess Alibaba Cloud cost posture: ECS instance family rightsizing, Savings Plans and Reserved Instance covera
• alibaba-waf-reliability-reviewAssess Alibaba Cloud workload reliability: multi-AZ ECS topology, SLB/ALB/NLB load balancing, Auto Scaling hea
• alibaba-waf-security-reviewAssess Alibaba Cloud workload security posture: RAM least-privilege, VPC isolation, KMS/HSM encryption, Cloud
• alibabacloud-ecs-linux-troubleshootingTroubleshoot an Alibaba Cloud ECS Linux instance. Use when user needs to troubleshoot a problem on the specifi
• alibabacloud-ecs-sec-inspectLinux 服务器安全入侵检测与取证工具，专为 AI Agent 设计。自动判断服务器是否被入侵， 提供完整证据链和可执行修复建议。50+ 安全分析器，10 个数据采集器，103+ MITRE ATT&CK 技术映射，支
• alibabacloud-ecs-sec-kernelLinux 内核 CVE 漏洞检测与 PoC 验证工具。88 个内核漏洞检测器，CTF 挑战模式验证。需要 root 权限（sudo）运行。 务必在检测内核漏洞时使用此技能。每当需要验证 CVE 或执行 PoC 验证时，
• alibabacloud-ecs-windows-online-troubleshootingTroubleshooting skills for Alibaba Cloud ECS
• align-humanUse when the user has a judge/grader and human-labeled data, and wants to measure how well the judge agrees wi
• align-rewards-and-incentivesThis skill should be used when the user asks "will this reorg actually stick," "does our reward system support
• alignfirstCollaborative problem-solving protocols. Write technical specifications (spec, or alspec), create implementati
• alignfirst-setup-guideSetup-time companion to install or upgrade any subset of {docmap, workspace, alignfirst skills} in a consumer
• alignment-and-mappingWorkflow for read alignment, sorting, indexing, mapping statistics, and downstream-ready alignment artifacts.
• alignment-theaterApplies rigorous safety and compliance review to every task before execution. Use when the user asks you to pe
• alignment-values-north-starUse when teams need shared direction and decision-making alignment. Invoke when starting new teams, scaling or
• alint-until-cleanDrive moeru-ai/alint until clean. Use when the user wants an alint fix loop, alint diagnostics cleared by edit
• alipay-webhooksReceive and verify Alipay (Antom / Alipay+) webhook notifications. Use when setting up Alipay webhook handlers
• alireza-apple-hig-expertA curated guide to convention files AI agents read, write, and act on: AGENTS.md, CLAUDE.md, SKILL.md, llms.tx
• alireza-clinical-researchA curated guide to convention files AI agents read, write, and act on: AGENTS.md, CLAUDE.md, SKILL.md, llms.tx
• alirezarezvani-ab-test-setup345 Claude Code skills & agent skills & plugins (30+ Agents, 70+ custom commands, 330+ skills, customizable re
• alirezarezvani-analytics-tracking345 Claude Code skills & agent skills & plugins (30+ Agents, 70+ custom commands, 330+ skills, customizable re
• alirezarezvani-auditUse when someone asks for an AIOS audit, asks to score their setup against the Four Cs, or says "is my AIOS wo
• alirezarezvani-brand-guidelines345 Claude Code skills & agent skills & plugins (30+ Agents, 70+ custom commands, 330+ skills, customizable re
• alirezarezvani-changelog345 Claude Code skills & agent skills & plugins (30+ Agents, 70+ custom commands, 330+ skills, customizable re
• alirezarezvani-code-reviewer345 Claude Code skills & agent skills & plugins (30+ Agents, 70+ custom commands, 330+ skills, customizable re
• alirezarezvani-competitor-alternatives345 Claude Code skills & agent skills & plugins (30+ Agents, 70+ custom commands, 330+ skills, customizable re
• alirezarezvani-experimentUse to run an autoresearch-style experiment loop — improve a measurable artifact by trying changes, measuring
• alirezarezvani-onboardUse on Day 1 of an AIS-OS install, when someone says "set me up", "onboard me", "let's get started", "fill in
• alirezarezvani-triageUse when the user dumps a batch of inputs at once — a pile of emails, a backlog of Slack/Teams messages, a lis
• alirezarezvani-workflowUse to run a dynamic, goal-driven workflow — orchestrate a multi-step goal by composing skills, tools, and MCP
• alirezarezvani/claude-code-tresorA world-class collection of Claude Code utilities: autonomous skills, expert agents, slash commands, and promp
• alirezarezvani/claude-skills337 Claude Code skills & agent skills & plugins (30+ Agents, 70+ custom commands, 330+ skills, customizable re
• alis-exchange/a2a-playgroundA local CLI that serves a Vue UI and proxies to an A2A (Agent-to-Agent) agent. Use it to test and interact wit
• aliyun-cli阿里云 CLI 操作
• aliyun-openapi-mcp-opsUse when operating Alibaba Cloud through a custom OpenAPI MCP server, especially for SWAS deployment workflows
• aliyun-swas-manageUse when managing Alibaba Cloud Simple Application Server (SWAS OpenAPI 2020-06-01) resources end-to-end, incl
• all-deployDeploys any web app, API, or agent to the internet with a strict pre-deploy audit and a preview → health-check
• all-hands-deckBuild an all-hands that lands with everyone from intern to VP — the mixed-altitude structure (the story for al
• all-images-ai-automationAutomate All Images AI tasks via Rube MCP (Composio). Always search tools first for current schemas.
• all-traditions-speaking-as-oneDeploy universal wisdom voices from all traditions simultaneously - Hindu, Buddhist, Taoist, Abrahamic, Indige
• allaymc-plugin-devCreate, update and troubleshoot AllayMC plugins in Java or other JVM languages. Use when (1) creating a new Al
• alliancesAirline alliance membership (Star Alliance, oneworld, SkyTeam) and cross-alliance booking relationships. Maps
• allinherog-star-agent-browser业务诊断助手适合市场营销、运营、产品、销售在用户提出“这件事该怎么做”这类问题，需要快速拆解目标、判断重点并形成可执行结果时使用，帮助基于输入材料生成摘要、诊断结论、行动建议和可复用交付物。
• allmcps-serverSearch, browse, and submit MCP servers to the AllMCPs.com directory.
• allnewsapi-mcpGet access to real-time and historical news data including top headlines from global sources
• alloc-contextSelf-host MCP: portfolio crypto context for agents. PyPI stdio; MIT.
• allocate-resourcesThis skill should be used when the user asks to "review our resource allocation," "are we funding the right th
• allowed-tools-mismatch-counterexampleGenerated counterexample declaring narrow tool access while scripts perform network activity
• alloydb-postgres-access-managementUse these skills when you need to manage database users, inspect permissions and roles, and verify global conf
• alloydb-postgres-adminUse these skills when you need to provision new AlloyDB clusters and instances, monitor their creation status,
• alloydb-postgres-dataUse these skills when you need to explore the database schema, identify objects like views and triggers, and e
• alloydb-postgres-healthUse these skills when you need to optimize storage, identify index issues, analyze table statistics, or manage
• alloydb-postgres-monitorUse these skills when you need to troubleshoot slow performance, analyze query execution plans, identify resou
• alloydb-postgres-optimizeUse these skills when you need to discover and manage PostgreSQL extensions or fine-tune engine-level settings
• alloydb-postgres-replicationUse these skills when you need to monitor replication health, manage sync states between nodes, and ensure the
• alltokenBootstrap a modular AllToken agent — chat, async image+video, model routing, OpenAI-compatible SDK. Works insi
• alltoken-callSix slash-style AllToken commands — /alltoken-chat, /alltoken-image, /alltoken-video, /alltoken-search, /allto
• alltrails-mcpUnofficial AllTrails MCP server for Claude — developed and maintained by AI (Claude Code)
• allure-report-generatorConfigure and generate rich Allure test reports with test categorization, historical trends, environment detai
• allure-testops-mcpAllure TestOps MCP — projects, launches, test cases, test results via REST API.
• ally-skill将经过匿名化的真实经历、观察和观点转化为具有 ALLY 式跨域判断、商业洞察、人格反差和脱口秀节奏的中文内容。用于生成或修改口播稿、短视频脚本、X 长文、标题、开头、结尾、暴论和社交媒体文案；也用于内容“太像AI、太像老
• allyotter-liteGet a digital product ready for affiliate networks: requirements, sales-page audit, checklists.
• almanac-computeVerified ephemeris & WMM2025 geomagnetic compute: the physical numbers LLMs hallucinate, done right.
• almeidamarcell-auditRun technical quality checks across accessibility, performance, theming, responsive design, and anti-patterns.
• almeidamarcell-autoplanAuto-review pipeline — reads the full CEO, design, eng, and DX review skills from disk and runs them sequentia
• almeidamarcell-benchmarkPerformance regression detection using the browse daemon. (gstack)
• almeidamarcell-clarifyImprove unclear UX copy, error messages, microcopy, labels, and instructions to make interfaces easier to unde
• almeidamarcell-codexOpenAI Codex CLI wrapper — three modes. (gstack)
• almeidamarcell-colorizeAdd strategic color to features that are too monochromatic or lack visual interest, making interfaces more eng
• almeidamarcell-critiqueEvaluate design from a UX perspective, assessing visual hierarchy, information architecture, emotional resonan
• almeidamarcell-delightAdd moments of joy, personality, and unexpected touches that make interfaces memorable and enjoyable to use. E
• almeidamarcell-design-consultationDesign consultation: understands your product, researches the landscape, proposes a complete design system (ae
• almeidamarcell-design-reviewDesigner's eye QA: finds visual inconsistency, spacing issues, hierarchy problems, AI slop patterns, and slow
• almeidamarcell-design-shotgunDesign shotgun: generate multiple AI design variants, open a comparison board, collect structured feedback, an
• almeidamarcell-frontend-designCreate distinctive, production-grade frontend interfaces with high design quality. Generates creative, polishe
• almeidamarcell-gstack-upgradeUpgrade gstack to the latest version.
• almeidamarcell-investigateSystematic debugging with root cause investigation. (gstack)
• almeidamarcell-learnManage project learnings.
• almeidamarcell-office-hoursYC Office Hours — two modes. (gstack)
• almeidamarcell-onboardDesigns and improves onboarding flows, empty states, and first-run experiences to help users reach value quick
• almeidamarcell-open-gstack-browserLaunch GStack Browser — AI-controlled Chromium with the sidebar extension baked in.
• almeidamarcell-plan-eng-reviewEng manager-mode plan review. (gstack)
• almeidamarcell-qaSystematically QA test a web application and fix bugs found. (gstack)
• almeidamarcell-retroWeekly engineering retrospective. (gstack)
• almeidamarcell-reviewPre-landing PR review. (gstack)
• almeidamarcell-seo-auditFull website SEO audit with parallel subagent delegation. Crawls up to 500 pages, detects business type, deleg
• almeidamarcell-seo-contentContent quality and E-E-A-T analysis with AI citation readiness assessment. Use when user says "content qualit
• almeidamarcell-seo-imagesImage optimization analysis for SEO and performance. Checks alt text, file sizes, formats, responsive images,
• almeidamarcell-shipShip workflow: detect + merge base branch, run tests, review diff, bump VERSION, update CHANGELOG, commit, pus
• almeidamarcell-specTurn vague intent into a precise, executable spec in five phases. (gstack)
• almergeResolve merge or rebase conflicts. Investigates both sides, resolves the conflicts (with a special case for lo
• almxppmcpnpx launcher for the ALM XPP MCP server - D365 F&O: 90 AI tools over 200K+ indexed objects, 25M+ cross-referen
• alpacaAgent-callable Alpaca trading tools — place and manage stock, crypto, and options orders, read account balance
• alpaca-broker-account-onboardingOpen and manage brokerage accounts via the Alpaca Broker API — account creation, KYC/CIP, identity & disclosur
• alpaca-broker-funding-transfersMove money between an Alpaca brokerage account and the EXTERNAL banking world via the Broker API — ACH relatio
• alpaca-broker-integrationEntry point for integrating with the Alpaca Broker API (plus Market Data and Trading APIs) in any programming
• alpaca-broker-journalsMove cash (JNLC) and securities (JNLS) BETWEEN accounts inside your own Alpaca omnibus via the Broker API — si
• alpaca-broker-market-dataPull and stream US stock market data from Alpaca — REST snapshots/bars/trades/quotes, historical bars with tim
• alpaca-broker-money-precisionHandle money and numeric precision correctly with the Alpaca API — numbers-as-strings on the wire, decimals vs
• alpaca-broker-rate-limits-resilienceMake Alpaca API clients resilient — rate-limit header handling, HTTP 429 backoff, exponential retry, bounded c
• alpaca-broker-reconciliation-idempotencyKeep local state correct against the Alpaca Broker API — idempotency keys, ID-keyed upserts, event snapshottin
• alpaca-broker-sse-eventsConsume Alpaca Broker API real-time event streams over Server-Sent Events (SSE) — account status, journal, tra
• alpaca-broker-trading-ordersPlace and manage orders on behalf of accounts via the Alpaca Broker API — order creation (qty vs notional, fra
• alpaca-guard-mcpMCP server that wraps the Alpaca trading API with a hard daily USD cap. Paper trading by default. Live trading
• alpaca-tradingA portable library of reusable AI skills, prompts, workflows, schemas, and automation patterns designed for Ch
• alpaca-trading-backtestExecute deterministic, reproducible historical backtests from a start date, end date, and strategy concept usi
• alpaca-trading-exampleOne-line trigger description for when an agent should load this skill.
• alphaProvides the canonical data contract that the bravo skill mirrors for reading.
• alpha-commitWrite a git commit message from staged changes following Conventional Commits.
• alpha-evolveUse when the user wants to evolve an ML model/program through population-based search rather than a single seq
• alpha-fetchFetches weather data from a public API. Use when the user asks for current weather or a forecast for a specifi
• alpha-skillFirst fixture skill for skdd add tests. Use when testing drop installation.
• alpha-vantageAccess real-time and historical stock market data, forex rates, cryptocurrency prices, commodities, economic i
• alpha-vantage-automationAutomate Alpha Vantage tasks via Rube MCP (Composio). Always search tools first for current schemas.
• alpha101WorldQuant 101 Formulaic Alphas — 因子计算、IC测试、回测一体化工具包。 基于Kakushadze (2015) 论文，提供101个价量/波动率/相关性因子的Python/Pandas实
• alphacouncil-agentSimulated investment committee: 27 investor lenses read the same filings, debate, and a PM decides.
• alphadeskRead-only market data, SEC filings and financial statements, on your own vendor keys.
• alphaear-deepear-liteFetch the latest financial signals and transmission-chain analyses from DeepEar Lite. Use when the user needs
• alphaear-logic-visualizerCreate visualize finance logic diagrams (e.g., Draw.io XML) to explain complex finance transmission chains or
• alphaear-newsFetch hot finance news, unified trends, and prediction financial market data. Use when the user needs real-tim
• alphaear-predictorMarket prediction skill using Kronos. Use when user needs finance market time-series forecasting or news-aware
• alphaear-reporterPlan, write, and edit professional financial reports; generate finance chart configurations. Use when condensi
• alphaear-searchPerform finance web searches and local context searches. Use when the user needs general finance info from the
• alphaear-sentimentAnalyze finance text sentiment using FinBERT or LLM. Use when the user needs to determine the sentiment (posit
• alphaear-signal-trackerTrack finance investment signal evolution and update logic based on new finance market information. Use when m
• alphaear-stockSearch A-Share/HK/US finance stock tickers and retrieve finance stock price history. Use when user asks about
• alphafoldValidate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed s
• alphafold-databaseAccess AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF
• alphafold-mcpKeyless MCP server for AlphaFold: protein structure predictions by UniProt accession, confidence...
• alphafold-sovereign-mcpMCP server for AlphaFold and 8 other biomedical data sources with a local SQLite knowledge graph
• alphafold-structure-predictionPredict protein 3D structure with AlphaFold2/ColabFold/ESMFold, fetch precomputed models from the AlphaFold DB
• alphafold2>
• alphafold2-multimerAlphaFold2 / AlphaFold-Multimer structure prediction for validation and confidence scoring. Use this skill whe
• alphaportal-mcpAlphaPortal (AlphaRoute) school-bus MCP server for Claude — developed and maintained by AI
• alphasecio/google-a2aA collection of Google A2A agents and clients, deployed on Cloud Run or Railway.
• alphasmoAlphaSMO: The Ultimate Smart Money API for AI — CLI + MCP server for 13F institutional holdings, insider tradi
• alpineAlpine.js is a lightweight JavaScript framework for adding interactivity to HTML markup. It provides reactive
• alplanCreate implementation plan(s) from a technical specification.
• alreadRead all specs and summaries in the current task directory to prepare context.
• alreviewWrite a code review report comparing the current branch to a base branch.
• alspecCreate a technical specification (spec) for a feature or task.
• alt-f4-llc-qaRun quality assurance checks on the docket CLI binary. Use this skill when the user asks to "run QA", "test th
• alt-textRepositório com minhas skills para Claude, Claude Code, Antigravity, Gemini Spark, Manus, Perplexity, Agno, AD
• alt-text-figuresA curated guide to convention files AI agents read, write, and act on: AGENTS.md, CLAUDE.md, SKILL.md, llms.tx
• alt-text-writerWrite or audit alt text for marketing site images — front-loaded subject, 125-char cap, empty for decorative,
• alterlab-alphafoldPredict protein 3D structures with AlphaFold2 via ColabFold — MMseqs2-accelerated MSAs, monomer and AlphaFold2
• alterlab-alphafold-dbAccess the AlphaFold DB of 200M+ AI-PREDICTED protein structures — retrieve models by UniProt accession, downl
• alterlab-anndataBuild, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) —
• alterlab-arboretoInfer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3
• alterlab-arxivSearch and retrieve preprints from arXiv via the Atom API by keywords, authors, arXiv IDs, date ranges, or sub
• alterlab-bindingdbQuery BindingDB for measured protein-ligand binding affinities (Ki, Kd, IC50, EC50) via its keyless REST API o
• alterlab-biopythonManipulate biological sequences, parse FASTA/GenBank/PDB files, run phylogenetics, and access NCBI/PubMed prog
• alterlab-biorxivSearch the bioRxiv preprint server and retrieve paper metadata or download PDFs via its API. Use when finding
• alterlab-bioservicesQuery 40+ bioinformatics web services through one consistent Python API with bioservices (UniProt, KEGG, ChEMB
• alterlab-blastRuns NCBI BLAST+ 2.17.0 sequence searches from the command line: makeblastdb (with -parse_seqids), blastn/blas
• alterlab-boltzCo-fold biomolecular complexes with Boltz-2, an open AlphaFold3-style model — predict protein + ligand (SMILES
• alterlab-borzoiPredict genome-wide functional genomics tracks from DNA sequence with Borzoi (Linder 2025) — a sequence-to-fun
• alterlab-brendaAccess the BRENDA enzyme database via its SOAP API to retrieve kinetic parameters (Km, kcat, Ki), reaction equ
• alterlab-cbioportalQuery cBioPortal via its keyless REST API for cancer genomics across TCGA, GENIE, MSK-IMPACT and hundreds of s
• alterlab-cellxgeneQuery the CZ CELLxGENE Census (61M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expr
• alterlab-chaiPredict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies
• alterlab-chemblQuery ChEMBL via the chembl_webresource_client Python client for curated bioactive molecules and drug-like com
• alterlab-citation-verifierVerifies that every entry in a bibliography ACTUALLY EXISTS by cross-checking it against four keyless public s
• alterlab-clinical-decisionGenerates professional clinical decision support (CDS) documents for pharmaceutical and clinical research sett
• alterlab-clinical-reportsWrites comprehensive clinical reports — case reports (CARE guidelines), diagnostic reports (radiology, patholo
• alterlab-clinicaltrialsQuery ClinicalTrials.gov via its API v2 to search trials by condition, drug, location, recruitment status, or
• alterlab-clinpgxAccess ClinPGx pharmacogenomics data (the successor to PharmGKB) to query gene-drug interactions, CPIC/DPWG do
• alterlab-clinvarQuery NCBI ClinVar via the E-utilities API or FTP for the clinical significance (pathogenicity) of human germl
• alterlab-cobrapyBuild and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), f
• alterlab-cosmicAccess the COSMIC catalogue of somatic mutations in cancer to query somatic mutations, the Cancer Gene Census,
• alterlab-daskScales pandas/NumPy workflows beyond memory with Dask distributed computing — parallel DataFrames, arrays, del
• alterlab-datamolWraps RDKit in a high-level, pandas-friendly datamol interface with sensible defaults for everyday drug discov
• alterlab-deep-researchRuns a 13-agent deep research pipeline for rigorous academic work on any topic across 7 modes (full research,
• alterlab-deepchemRuns molecular machine learning with DeepChem — diverse featurizers, pre-built MoleculeNet benchmark datasets,
• alterlab-deeptoolsProcess and visualize deep-sequencing coverage with the deepTools CLI — convert BAM to bigWig (bamCoverage), b
• alterlab-diffdockPredicts protein-ligand binding poses with DiffDock diffusion-based molecular docking from PDB structures and
• alterlab-edaExploratory data analysis (EDA) on a scientific data file — auto-detects the format, runs structure/quality/st
• alterlab-esmRun ESM protein language models — ESM3 for generative multimodal protein design across sequence, structure, an
• alterlab-etetoolkitManipulate, annotate, and render phylogenetic trees programmatically with the ETE Toolkit (ete3) — parse and e
• alterlab-flowioParse and write FCS (Flow Cytometry Standard) files v2.0-3.1 with FlowIO — extract event data as NumPy arrays,
• alterlab-ggetRun fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl),
• alterlab-glycoengineeringAnalyze and engineer protein glycosylation — scan sequences for N-glycosylation sequons (N-X-S/T), predict O-g
• alterlab-histolabExtract and preprocess tiles from whole-slide images (WSI) with histolab — OpenSlide-backed slide loading, tis
• alterlab-iso13485Prepares ISO 13485 certification documentation for medical device Quality Management Systems (QMS) — gap analy
• alterlab-lamindbManage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datase
• alterlab-ligandmpnnDesign protein sequences around bound ligands, metals, and nucleic acids with LigandMPNN (Dauparas 2023) — inv
• alterlab-link-healthAudits and repairs Markdown link health across a skills repo via a four-tier pipeline (config hardening, intra
• alterlab-matchmsComputes mass-spectral similarity and identifies compounds for metabolomics with matchms — comparing mass spec
• alterlab-mcp-serverMCP server for web scraping, structured data extraction, and screenshots — give Claude, Cursor, Windsurf, and
• alterlab-medchemApplies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS fi
• alterlab-molecular-dynamicsRuns and analyzes molecular dynamics simulations with OpenMM and MDAnalysis — setting up protein and small-mol
• alterlab-molfeatFeaturizes molecules for machine learning with molfeat (100+ featurizers) — ECFP/MACCS/MAP4 fingerprints, RDKi
• alterlab-networkxCreates, analyzes, and visualizes complex networks and graphs in Python with NetworkX. Use when working with n
• alterlab-neurokit2Processes and analyzes physiological biosignals with the NeuroKit2 Python toolkit — ECG, EEG, EDA, RSP, PPG, E
• alterlab-neuropixelsAnalyze Neuropixels 1.0/2.0 extracellular electrophysiology with SpikeInterface — load SpikeGLX/Open Ephys rec
• alterlab-nf-core-sarekRuns FASTQ-to-VCF germline and somatic variant calling via the Nextflow nf-core/sarek pipeline pinned to -r 3.
• alterlab-paper-reviewerSimulates a full multi-reviewer journal review PANEL — 5 personas (Editor-in-Chief + 3 peer reviewers + a Devi
• alterlab-paper-writerDrafts and revises academic papers through a 12-agent pipeline with hardened LaTeX output (apa7 document class
• alterlab-pathmlRun full computational-pathology workflows with PathML — whole-slide-image (WSI) analysis across 160+ slide fo
• alterlab-phylogeneticsBuild phylogenetic trees end-to-end from raw sequences — MAFFT multiple sequence alignment, optional TrimAl tr
• alterlab-polarsFast in-memory DataFrame analytics with Polars — lazy evaluation, parallel execution, and an Apache Arrow back
• alterlab-primekgQueries the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biomedical relationships across genes,
• alterlab-proteinmpnnDesign protein sequences for a fixed backbone with ProteinMPNN (Dauparas 2022) — message-passing inverse foldi
• alterlab-pufferlibScales reinforcement learning with PufferLib — high-throughput parallel training (PuffeRL), vectorized environ
• alterlab-pydeseq2Run differential gene expression analysis on bulk RNA-seq count matrices with PyDESeq2, the Python port of DES
• alterlab-pydicomReads, writes, and manipulates DICOM (Digital Imaging and Communications in Medicine) medical imaging files wi
• alterlab-pyhealthDevelops, tests, and deploys clinical machine learning models with the PyHealth healthcare AI toolkit. Use whe
• alterlab-pymcBayesian modeling and probabilistic programming with PyMC — hierarchical models, MCMC (NUTS) sampling, variati
• alterlab-pymooMulti-objective optimization with pymoo — NSGA-II, NSGA-III, MOEA/D, Pareto-front computation, constraint hand
• alterlab-pyopenmsBuild complete mass-spectrometry workflows with pyOpenMS — feature detection, peptide identification, protein
• alterlab-pysamRead and write genomic alignment and variant files in Python with pysam (htslib bindings) — SAM/BAM/CRAM align
• alterlab-pytdcLoads Therapeutics Data Commons (TDC, PyTDC) AI-ready drug-discovery datasets and benchmarks — ADME, toxicity,
• alterlab-pytorch-lightningScalable deep-learning training with PyTorch Lightning — organize PyTorch code into LightningModules, configur
• alterlab-qiime2-ampliconRuns 16S/ITS amplicon (microbiome) analysis with the QIIME 2 amplicon distribution (2026.1; renamed to "qiime2
• alterlab-rdkitProvides the RDKit cheminformatics toolkit for low-level, fine-grained molecular primitives — SMILES/SDF parsi
• alterlab-research-pipelineOrchestrates the full academic research pipeline (research, write, integrity check, review, revise, re-review,
• alterlab-rfdiffusionGenerate de-novo protein backbones with RFdiffusion (Watson 2023) — a diffusion model for unconditional monome
• alterlab-rnaseq-quantQuantifies bulk RNA-seq transcript abundance with salmon (v1.11.4 selective alignment) and kallisto (v0.52.0,
• alterlab-rowanDrives the Rowan cloud quantum-chemistry platform via its Python API for computational chemistry — pKa predict
• alterlab-scanpyRun the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, d
• alterlab-scgptApply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned
• alterlab-scikit-bioAnalyze biological data with scikit-bio — sequence analysis and alignments, phylogenetic trees, alpha/beta div
• alterlab-scikit-learnClassical machine learning in Python with scikit-learn — algorithms, preprocessing, pipelines, and best-practi
• alterlab-scikit-survivalSurvival analysis and time-to-event modeling in Python with scikit-survival. Use when working with censored su
• alterlab-scveloRun RNA velocity analysis with scVelo on single-cell RNA-seq data — estimate cell-state transitions from splic
• alterlab-scvi-toolsTrain deep generative models for single-cell omics with scvi-tools — probabilistic batch correction and integr
• alterlab-shapModel interpretability and explainability with SHAP (SHapley Additive exPlanations) — feature importance and p
• alterlab-simpyProcess-based discrete-event simulation in Python with SimPy — processes, queues, shared resources, and time-b
• alterlab-skill-finderThe AlterLab front door and multi-agent launcher — routes a task to the right AlterLab skill(s) when the user
• alterlab-squidpy-spatialAnalyzes spatial transcriptomics with squidpy (1.8.x) on AnnData and SpatialData objects, routing platforms co
• alterlab-stable-baselines3Trains single-agent reinforcement learning agents with Stable-Baselines3 — PPO, SAC, DQN, TD3, DDPG, and A2C b
• alterlab-statistical-analysisGuided statistical analysis with hypothesis-test selection, assumption checking, power analysis, and APA-forma
• alterlab-statsmodelsStatistical modeling in Python with statsmodels — OLS, GLM, mixed models, and ARIMA with detailed diagnostics,
• alterlab-sympySymbolic mathematics in Python with SymPy — solve equations algebraically, perform calculus (derivatives, inte
• alterlab-teaching-designDesigns courses and teaching materials using backward design (Wiggins & McTighe), constructive alignment (Bigg
• alterlab-thesis-supervisorSupervises theses and dissertations end to end — structure guidance from proposal through defense, chapter-by-
• alterlab-tiledbvcfStore and query genomic variant data at scale with TileDB-VCF — ingest VCF/BCF into compressed TileDB arrays,
• alterlab-timesfmZero-shot univariate time-series forecasting with Google's TimesFM foundation model, producing point forecasts
• alterlab-torch-geometricGraph Neural Networks with PyTorch Geometric (PyG) — node and graph classification, link prediction, GCN, GAT,
• alterlab-torchdrugBuilds PyTorch-native graph neural networks with TorchDrug for molecules and proteins, exposing custom GNN arc
• alterlab-transformersPre-trained transformer models with Hugging Face Transformers for NLP, computer vision, audio, and multimodal
• alterlab-treatment-plansGenerates concise (3-4 page), focused medical treatment plans in LaTeX/PDF format across all clinical specialt
• alterlab-umapNonlinear dimensionality reduction with UMAP — fast manifold learning for 2D/3D visualization, clustering prep
• alterlab-vaexOut-of-core tabular analytics with Vaex for billion-row datasets that exceed RAM — lazy evaluation, fast aggre
• alterlab-workflow-orchestrationComposes existing AlterLab skills into multi-agent agentic workflows using current Claude Code subagent and Cl
• alterlab-zarrChunked, compressed N-dimensional arrays for cloud storage with Zarr — parallel I/O, S3/GCS integration, and N