Results for “cellxgene”

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

Spatial region-aware cell matching for CODEX/scRNAseq integration

Queries the ClinPGx REST API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels, generating markdown reports with CSV tables.

Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels.

Fast structured generation and serving for LLMs with RadixAttention prefix caching. Use for JSON/regex outputs, constrained decoding, agentic workflows with tool calls, or when you need 5× faster inference than vLLM with prefix sharing. Powers 300,000+ GPUs at xAI, AMD, NVIDIA, and LinkedIn.

Fast structured generation and serving for LLMs with RadixAttention prefix caching. Use for JSON/regex outputs, constrained decoding, agentic workflows with tool calls, or when you need 5× faster inference than vLLM with prefix sharing. Powers 300,000+ GPUs at xAI, AMD, NVIDIA, and LinkedIn.

Explains cellular structures, membrane transport, energetics, signaling, and division, connecting molecular events to organismal function.

XState Typegen

Nx smart monorepo build system reference. Covers affected commands, computation caching, project graph visualization, nx.json and project.json config, code generators for React/ Angular/Node/Next.js, module boundary enforcement, Nx Cloud remote caching, and migration from Turborepo.

Use when triaging a study before any writing — stress-tests whether it clears Cell's bar (a complete, mechanistic, hypothesis-driven story with multiple converging lines of evidence) or belongs at a sibling. Use this first to decide Cell vs Molecular Cell vs Cell Reports vs Cell Reports Medicine before investing in framing or figures.

Identifies a medication from a photo and generates a genotype-informed dosage card using CPIC guidelines and real 23andMe data.

Nx build system and monorepo tools. Advanced task orchestration, generators, and plugins. Use for complex enterprise monorepos with multiple technologies. USE WHEN: user mentions "Nx", "nx.json", "Nx monorepo", "Nx generators", asks about "Nx workspace", "affected commands", "module boundaries" DO NOT USE FOR: Turborepo (use turborepo skill), simple monorepos (Turborepo is simpler), single-package projects

Fast structured generation and serving for LLMs with RadixAttention prefix caching. Use for JSON/regex outputs, constrained decoding, agentic workflows with tool calls, or when you need 5× faster inference than vLLM with prefix sharing. Powers 300,000+ GPUs at xAI, AMD, NVIDIA, and LinkedIn.

Access ClinPGx pharmacogenomics data (the successor to PharmGKB) to query gene-drug interactions, CPIC/DPWG dosing guidelines, drug labels, and pharmacogene records. Use when interpreting pharmacogenes (CYP2D6, CYP2C19, TPMT, DPYD, SLCO1B1), looking up genotype-guided drug dosing, checking PGx drug-safety associations (e.g. HLA-B*57:01 and abacavir), or supporting precision medicine and clinical pharmacogenomics decisions. For star-allele definitions/frequencies see PharmVar; for germline/somatic variant pathogenicity see alterlab-clinvar. Part of the AlterLab Academic Skills suite.

Generates a personalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) by interrogating nutritionally-relevant SNPs and producing actionable dietary guidance, all computed locally.

MaxFuse parameter tuning for datasets with large protein:RNA cell ratios (>100:1)

Use when deciding which cell-* sub-skill to invoke next, or when sequencing a manuscript from significance test through reviewer rebuttal for Cell (Cell Press). Routes — it does not replace — the specialized skills.

Write effective unit tests with modern MSTest 3.x/4.x, covering assertion APIs, data-driven tests, and test lifecycle best practices.

Scaffolds an xUnit integration test project for validating Oracle-to-PostgreSQL database migration behavior in .NET solutions, including transaction-rollback base class and seed data manager.

Helixa — Onchain identity, reputation, and Cred Scores for AI agents on Base. Use when an agent wants to mint an identity NFT, check its Cred Score, verify social accounts, update traits/narrative, query agent reputation data, check staking info, or search the agent directory. Supports SIWA (Sign-In With Agent) auth and x402 micropayments. Also use when asked about Helixa, AgentDNA, ERC-8004, Cred Scores, $CRED token, or agent identity.

CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.

Creates, analyzes, and visualizes complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing topologies — applicable to social, biological, transportation, citation, and any pairwise-relationship networks. This is classical graph analytics, not deep learning — for training graph neural networks (GCN/message passing, node/edge/graph classification on Cora-style data) use alterlab-torch-geometric instead. Part of the AlterLab Academic Skills suite.

CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.

Deploy and configure Xray proxy servers. Use when a user asks to set up VLESS, VMess, Trojan, or Shadowsocks proxies, configure Reality or TLS transport, deploy Xray with XTLS, set up fallback routing, manage multi-user access, configure traffic routing rules, set up CDN-based tunneling, build subscription links for client apps, monitor Xray traffic, or bypass network restrictions. Covers all major Xray protocols, transports, and deployment patterns.

CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.

Serve LLMs and VLMs with structured outputs, prefix caching, and high throughput using RadixAttention.

Generate CSV, Markdown, and XLSX spreadsheets from structured tabular data.

Write and run analytical SQL queries against Redpanda SQL (Oxla), a distributed PostgreSQL-wire-compatible columnar database, including data loading, external sources, and type handling.

Generate PPTX presentations, DOCX documents, XLSX spreadsheets, and PDF reports from structured JSON input using PaperJSX.

Computes evidence-aware polygenic risk scores from local VCF or WGS files using the just-prs engine and a pinned local MCP server, with honest interpretation and model comparison.

Generate an XLSX inventory report with stock levels, reorder points, unit costs, and total value formulas for purchasing teams.

Drive mex (`mex-agent`), persistent project memory and code graphs for AI coding agents. One command scaffolds a living wiki, builds a deterministic code graph, and installs a project anchor file (CLAUDE.md, root AGENTS.md, .cursorrules, .windsurfrules, copilot-instructions.md, or .opencode/opencode.json) that your agent auto-loads as a standing rule document. Use when the user wants to `mex setup` a new project, build a symbol-grounded wiki, keep knowledge connected to implementation, route relevant context to agents, or run drift detection (`mex check`, `mex sync`). Triggers on: "mex setup", "project memory", "code graphs", "codebase documentation", "drift detection", "agent memory", "structured scaffolds", "architectural context", "living wiki", "project anchor file".

Runs and interprets Elixir/Phoenix tooling (mix test, credo, dialyzer, format), generates OTP-conforming modules, and helps with Ecto and LiveView patterns.

Returns structured prediction-market data for Polymarket, Kalshi, Limitless, Opinion, Predict.Fun, dFlow, and UMA oracle via a local API, covering markets, cross-venue search, leaderboards, smart money, wallet analytics, identity clustering, and resolution status.

FREE — God-tier long-context memory for AI agents. Injects 500K-1M clean tokens, auto-summarizes with tone/intent preservation, compresses 14-turn history into 800 tokens.