LLM Mart Basic

Generate de-novo protein backbones with RFdiffusion (Watson 2023) — a diffusion model for unconditional monomer generation, motif scaffolding, binder design against a target, and symmetric oligomers. Use when generating a new protein backbone from scratch, scaffolding a functiona

Quantifies bulk RNA-seq transcript abundance with salmon 2.x (the Rust rewrite; selective alignment or --sketch) and kallisto (v0.52.0, kb-python workflow), builds a decoy-aware gentrome index, runs quant with --gcBias -l A, then imports estimates via tximport/tximeta with a tx2g

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

A green PR, a controller reporting success, and not one line of the new code running

Discover testnet↔mainnet subnet lineage from repo configs and open a PR for review (pass --dry-run to report only)

Triage raw inbox notes into reviewed repository destinations without deleting their sources.

Audit and rewrite content to remove AI writing patterns

Log a completed piece of content to content/log.md after the user confirms it was published.

Validate a dream artifact, review each proposal, and apply only individually accepted changes.

Run a curator pass against the validated memory directory and produce a proposal artifact.

End a session — log what happened, update state and the decision log, propose memory updates, and check for uncommitted or unpushed work

Find relevant context files by topic. Use when you need to load files for a topic without a slash command, or when a task spans multiple domains.

Inventory and migrate selected Gemini CLI workflows with dry-run review and parity checks.

Find repeated workflows in selected Gemini CLI sessions and draft portable skills after review.

Scan multi-session drift and offer individually reviewed fixes only after explicit approval.

Scan orphaned worktrees and stale branches, then offer explicit approval-gated cleanup.

Guided onboarding or import for durable workspace context

Start a session — load state files, flag staleness, and give a briefing on current priorities, deadlines, and blockers

Create a morning heartbeat from repository state and update the local heartbeat log.

Mid-session checkpoint — append progress to today's session log and update state files if a priority shifted, without ending the session

Maintainer-only. Find every file that would newly ship to adopters, classify each one against the written distribution-boundary categories, default to withhold on no clean match, and ask the maintainer only where the taxonomy does not settle it. Drives the release CLI, which refuses to produce a manifest until every shipping file has an answer.

Audit memory, wiki, and auto-loaded files for duplication, conflicting instructions, and stale content. The default path researches, then asks you a single Apply / Discuss / Decline question; on Apply it applies the report, files any out-of-scope problem as a tech-debt issue, then commits, opens a PR, and merges it on a main-branch run like /update-deps. Pass --apply to re-run the apply-and-publish stage against the most recent report.

Fix the tech-debt backlog, a single issue or a recommended related batch, highest severity then oldest first, on a fresh isolated branch through the audit gate, closing the issue(s) on merge. Pass `list` to see the ordered backlog, `why <issue-number>` to explain the recommendation, or a bare `<issue-number>` to fix that issue directly.

Health-check and auto-heal this project's Claude integration, triage, heal, verify, and report an F-to-A+ grade.

🤖 MateClaw — Your second brain with Multi-Agent Orchestration, MCP Protocol, Skills & Memory, Dream, and Multi-Channel Support. Built on Spring AI Alibaba.

Vibe-Research: Your Personal Trading Research Agent · A股/美股/港股 的个人投研 Agent：每日复盘、资讯雷达、个股数据、板块中心、我的持仓、研究记录、回测。Vibe-Research 把数据和功能配齐，由你自己的 Agent 驱动投资研究。基于开源的 Code…

Wayland - The AI Agent That Perceives. Reasons. Acts. Evolves.

Observability and enforcement for AI agent harnesses. Capture every run and runtime reliability with policy enforcement. 40 built-in policies, a local dashboar…

Turn your Solana Seeker (or any Android phone) into a 24/7 personal AI agent

A curated collection of offensive, defensive and AI/LLM security tools.

AI agent 通用任务治理框架：对齐目标与事实，规划和调度能力，守住授权与风险边界，治理任务执行到真实验收与交付。Governance framework for evidence-driven planning, orchestration, and verified delivery.

Open-source (Apache-2.0) PDF takeoff for construction & flooring — the first engine an AI agent drives natively over MCP, not bolted on. One-click room detectio…

Stop degrading your model's reasoning. A minimal, zero-config AI coding agent. Enforced ephemeral subagents keep context pure. From tiny local models up to Sol,…

实习.skill — 双非也能拿大厂 offer。帮你改简历、抠面经、准备面试，把真实背景翻译成面试官想要的样子。

专门为 agent 打造的 agent 搜索工具，具备多语言搜索能力，覆盖中文/英文/学术/代码/购物/金融/新闻/百科。

Local-first AI agent workspace for multi-agent collaboration, agent orchestration, scoped permissions, evidence-aware runs, and human-in-the-loop decisions.

Keyboard-first desktop Kanban workspace for AI coding agents with embedded terminals, git worktrees, and hook-driven task tracking.

Claude Code Prompt Mechanism Visualizer — Electron desktop app

Multi-repo semantic code search MCP server in Rust — hybrid vector + BM25 retrieval, tree-sitter AST chunking, fully offline. For OpenCode, Claude Code, Cursor,…

One-ink editorial print image skill — warm paper, halftone photography, active negative space, and restrained typography.

US stock market data for AI coding assistants — zero-auth, official sources. CBOE options with full Greeks + 0DTE flow, FINRA market-wide short volume, SEC EDGA…

AI-powered Werewolf (Mafia) social deduction game where every player is controlled by top LLMs like DeepSeek, Qwen, Gemini, and more

A股全栈数据工具包 · 十一层架构 · 54端点 · 19数据源 · 零鉴权 | Full-stack China A-share data toolkit for AI agents — 11 layers, 54 endpoints, 19 sources, zero-auth

Agentic desktop GUI client for Elasticsearch, OpenSearch, DynamoDB, MongoDB & EasySearch. Natural language queries, visual management, and monitoring. Privacy-f…