LLM Mart Basic

Run the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, dimensionality reduction (PCA, UMAP, t-SNE), Leiden/Louvain clustering, marker/differential expression, PAGA trajectories, and plotting. Use when analyzing scRNA-seq data

Apply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData. Use when annotating cell types with a pretraine

Run RNA velocity analysis with scVelo on single-cell RNA-seq data — estimate cell-state transitions from spliced/unspliced mRNA dynamics, infer trajectory direction, compute latent time, and identify driver genes. Use when adding directionality to trajectories or studying differe

Train deep generative models for single-cell omics with scvi-tools — probabilistic batch correction and integration (scVI), reference-mapping transfer learning (scArches), differential expression with uncertainty, and multimodal models (totalVI for CITE-seq, MultiVI for multiome)

Analyzes spatial transcriptomics with squidpy (1.8.x) on AnnData and SpatialData objects, routing platforms correctly: Visium spots use spatial_neighbors(coord_type='grid') and pair with deconvolution, while Xenium/MERFISH single-cell data use coord_type='generic'/Delaunay neighb

Store and query genomic variant data at scale with TileDB-VCF — ingest VCF/BCF into compressed TileDB arrays, add samples incrementally, run fast parallel region/sample queries, and export back to VCF. Use when managing population-genomics variant datasets that are too large for

Wraps RDKit in a high-level, pandas-friendly datamol interface with sensible defaults for everyday drug discovery — SMILES/SDF loading into DataFrames, molecule standardization, descriptors, fingerprints, Butina clustering, 3D conformer generation, scaffold analysis, and parallel

Runs molecular machine learning with DeepChem — diverse featurizers, pre-built MoleculeNet benchmark datasets, and pre-trained models (ChemBERTa, GROVER) for property prediction (ADMET, toxicity, solubility) via traditional ML or graph neural networks. Use when running end-to-end

Predicts protein-ligand binding poses with DiffDock diffusion-based molecular docking from PDB structures and SMILES, producing pose confidence scores for virtual screening and structure-based drug design. Use when docking ligands into a protein, generating binding poses, or scre

Computes mass-spectral similarity and identifies compounds for metabolomics with matchms — comparing mass spectra, scoring similarity (cosine, modified cosine), and searching spectral libraries to annotate unknowns. Use when matching MS/MS spectra, identifying metabolites, or lib

Applies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, and molecular complexity metrics for compound prioritization and library cleanup. Use when filtering or triaging a compound library, flagging PA

Featurizes molecules for machine learning with molfeat — ECFP/MACCS/MAP4 fingerprints, RDKit and Mordred physicochemical descriptors, pharmacophore and shape descriptors, and pretrained embeddings (ChemBERTa, ChemGPT, CheMeleon) exposed as scikit-learn transformers that convert S

Queries the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biomedical relationships across genes, drugs, diseases, phenotypes, pathways, and biological processes. Use when exploring drug-disease or gene-disease links, building disease-centric knowledge subgraphs, or

Loads Therapeutics Data Commons (TDC, PyTDC) AI-ready drug-discovery datasets and benchmarks — ADME, toxicity, drug-target interaction (DTI), scaffold splits, and molecular oracles for therapeutic ML and pharmacological prediction. Use when fetching a standardized benchmark datas

Provides the RDKit cheminformatics toolkit for low-level, fine-grained molecular primitives — SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure/SMARTS search, 2D/3D coordinate generation, similarity, and reaction handling. Use when custom sanitization,

Drives the Rowan cloud quantum-chemistry platform via its Python API for computational chemistry — pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2), wi

Builds PyTorch-native graph neural networks with TorchDrug for molecules and proteins, exposing custom GNN architectures, task/dataset abstractions, molecular generation, retrosynthesis planning, and knowledge-graph reasoning. Use when a project specifically needs TorchDrug's dat

Generates professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings — biomarker-stratified patient cohort analyses with outcomes and evidence-based treatment recommendation reports with decision algorithms, supporting GRADE evidence

Prepares ISO 13485 certification documentation for medical device Quality Management Systems (QMS) — gap analysis of existing documentation, Quality Manuals, required procedures and work instructions, and Medical Device Files. Use for ISO 13485 QMS documentation, conducting a doc

Processes and analyzes physiological biosignals with the NeuroKit2 Python toolkit — ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements, or when

Fourteen posts of being wrong in production, compressed to checkboxes

Healthy nodes, a quiet network, 300 restarts in three days, and a latency budget measured in milliseconds

Discovery worked. Ping worked. Every TCP connection timed out, and later the tunnel only worked when someone had a terminal open.

Every VM came back. The cluster did not. Declarative systems converge on config, and the datapath isn't config.

A surprising share of AI-in-the-terminal failures aren't the AI. They're zsh, and a version of bash from 2006.

A Claude Code plugin turns standalone project configuration into a namespaced, installable extension that teams and communities can update as one unit.

None of the safety came from the model. It came from six boring habits.

Skills package instructions and references. Subagents run work in a separate context and return results. They solve different problems and can be composed deliberately.

Six hours in, one step left, everything green, and the incident that didn't happen

CLAUDE.md carries persistent project context. Skills load reusable procedures when relevant. Separating stable facts from task-specific workflows keeps both easier to maintain.

Twenty minutes recovering secrets that never existed, and the one sentence from a human that ended it

An API request routing a model's tool call through an approval gate to a remote MCP server

31 config keys, two audits, and why the first one was wrong in both directions

The official MCP Registry stores standardized server metadata rather than package code. Publishers verify a namespace, describe installation or remote access, and submit immutable versions.

Everyone looks at the Dockerfile. The file that actually leaked the key was the project file.

Remote MCP authorization uses established OAuth standards, but secure integration still requires issuer validation, least-privilege scopes, protected token handling, and server-side enforcement.

"Copy it over and switch the reference" is two steps, and the outage lives in the one nobody checks

stdio fits local processes and prototypes. Streamable HTTP fits hosted services and shared integrations. The right choice follows where the capability runs and who must reach it.

The most important rule wasn't about what I could change. It was about what I was allowed to display.

Tools perform operations, resources expose readable context, and prompts provide reusable templates. Choosing the correct primitive makes an MCP server easier to understand and govern.

Repeatable pass upgrading an Angular admin dashboard into a compact black-and-cyan developer-cockpit PWA

Run the drift-detection checklist (incl. agent-drift signals); report + fix in-turn

Orchestrate the final review fan-out (integration + diversity + risk + release readiness)

Run the AI-augmented lint self-improvement loop on the current project. Scans `.lint-history/` for recurring violation patterns (≥3 hits in 30d window), drafts a Claude-ready prompt to author a new semgrep rule for the top candidate, and surfaces the proposal under `.lint-history/proposals/<ts>.md`. Non-blocking analysis. See rules/lint-doctrine.md § Self-improving.

Bootstrap industry-leading lint+autofix+commit-hygiene stack on the current project. Drops in lefthook, oxlint, ESLint, Prettier, Stylelint, markdownlint, ruff, shellcheck, shfmt, yamllint, hadolint, actionlint, jscpd, knip, semgrep, gitleaks, commitizen + git-cz-emoji (emoji-mandatory commits), and semantic-release. Idempotent — re-runs upgrade safely. See rules/lint-doctrine.md.

Surface all retrospective documents with key shape metrics; compare arcs deliberately.

Progressive multimedia enrichment pass — add high-value audio/video/image/interactive to a site, run again and again

Run the autonomous-engineering operating loop on a task (plan→implement→verify→repair→report)

Capture the cumulative output of a /loop arc into a single auditable retrospective document; scans the heymegabyte-claude-skills plugin for modified files, categorizes by directory, counts LOC delta, extracts tool counts from MCP servers, and writes a timestamped report to retrospectives/

Turn a comma-separated list of file paths into a fully structured Pattern A agent brief — ordered writes, per-file schemas, and a verification step baked in.

Turn Pattern B from agent-resilience-discipline into a one-keystroke agent brief for a single-file deliverable < 300 lines.

Chain the full Superpowers process flow — brainstorm → plan → worktree → build → review → finish — on one slash command

Generate a timestamped arc retrospective from the past 7 days of git history in `~/.agentskills`.

Review ~/.claude/CLAUDE.md + rules for contradictions, stale guidance, duplication; consolidate

Batch-run all LLM eval cases in tools/evals/cases/*.json; aggregate pass/fail, cost, regression vs last run; exit nonzero in CI mode

One-line SaaS — from a description, scaffold a complete CF-native multi-tenant SaaS (Hono + D1 + Drizzle + Better Auth + Stripe + shadcn) deployed to a real URL

Unified supply-chain audit. Checks GitHub Actions SHA-pinning (`sha-pin:check`), package.json git+https deps (per `no-gitlab-megabytelabs-deps` semgrep), gitleaks scan, and trufflehog verified-only sweep. Surfaces any tag-mutable, git-URL, or secret-exposed surface. Per rules/ai-agent-security.md § Supply chain.

Run a learning pass after a major run; fold reusable lessons into global config

Summarize recent CHANGELOG.md entries for context restoration. Parses the canonical heading shape `## YYYY-MM-DD — pass-N — summary`. Filters: last N (default 10), YYYY-MM date prefix, or "today". Supports --json for machine-readable output.

Run quality-scores + token-budget + dep-graph, interpret results, flag missing budgets, orphans, and oversize skills

Open-source super AI assistant & Agent Harness. Plans tasks, runs tools and skills, self-evolves with memory and knowledge. Multi-model, multi-channel. Lightwei…

Open-source AI browser agent for web automation: a web browsing agent and computer-use agent in plain English. Browser MCP for Claude Code and Gemini CLI.

Agent-native trading terminal built on DeepSeek Harness. Crypto, US, CN and HK in one three-column GUI, 19+ hot-swappable connectors, dry-run by default with hu…

Open-source desktop and web coding agent with a first-party host and harness, durable sessions, model connections, streaming chat, and workspace tools.

OrcaReplay — Time travel for AI agents. Record, replay, fork, and debug any agent run with any model. Built by the OrcaRouter.ai team.

A complete toolkit for connecting R and LLMs

OpenSRE — the memory-first AI SRE. Self-hosted incident investigation with episodic memory, knowledge graph, web console, Slack & Teams. opensre.in

A desktop AI coding assistant that works with your local projects. Ally helps you understand code, edit files, search a workspace, manage tasks, and complete de…

【在线免费使用】 简单快速将SQL或DBML转换为美观的ER图（支持 Agent Skill）/ The best SQL to ER Diagram converter (Support Agent Skill).

Operation-bound protection for autonomous AI agents: contain and verify operations before committing changes, understand intent and risk across long-running wor…

Local-first AI coding agent desktop: Electron + Rust host core + pi Agent Harness + user-installable plugins

Local-only Go static analysis engine with a built-in MCP server. Gives AI coding agents deterministic structural awareness: call graphs, impact analysis, symbol…

Self-hosted AI agent workspace with tool calling, MCP, multi-model routing, sandboxed execution, multi-agent workflows, and LLM-authored 3D character animation…

Automated TDD enforcement for Claude Code

High-performance platform for building websites, e-commerce, and web applications—with Native AI, JavaScript development, and a marketplace for portable sites a…

Autonomous AI-agent orchestration engine for job discovery with decision traces, tool adapters, and production-grade run control.

Token efficient Claude Code full Python rebuild. AI Coding Agent in 310K LoC Python.

OPC — One Person Company. A full team in a single Claude Code skill. Adaptive agent orchestrator with 21 built-in roles, 6 flow templates, and adversarial quali…

Open-source, secure environment with real-world tools for enterprise-grade agents.

MCP server for AI-powered GitHub project management — agent orchestration, PRD-to-issues pipeline, sprint planning, and multi-agent swarm coordination