knowledge-graph commands

TianGzlab/OmicsClaw

Agent

Issues and PRDs for this repository live in GitHub Issues for zhou-1314/OmicsClaw. Use the gh CLI for issue operations.

TianGzlab/OmicsClaw

Agent

Engineering skills use five canonical triage roles. Each role maps directly to the corresponding GitHub label.

TianGzlab/OmicsClaw

Skill Claude CodeCodex

Systematic workflow for clustering biological samples, features, or any quantitative data matrix. Implements multiple clustering algorithms with rigorous validation, comparison, and interpretation to identify meaningful data groupings.

TianGzlab/OmicsClaw

Skill Claude CodeCodex

Core DESeq2 workflow for RNA-seq differential expression analysis with count data.

TianGzlab/OmicsClaw

Skill Claude CodeCodex

Complete workflow for single-cell RNA-seq analysis using Seurat v5. Process raw data through quality control, normalization, clustering, and cell type annotation with publication-ready visualizations.

dnotitia/akb

Plugin Claude Code

Plugin marketplace listing 3 plugins: akb-claude-code, akb-sessions, akb-wiki.

dnotitia/akb

Command Claude Code

Review AKB production-governance docs and hooks.

dnotitia/akb

Hook Claude Code

Runs when a session starts, executing akb_pm_hook.py via python3. From dnotitia/akb.

dnotitia/akb

Hook Claude Code

Runs when you submit a prompt, before the agent sees it, executing akb_pm_hook.py via python3. From dnotitia/akb.

dnotitia/akb

Hook Claude Code

Runs before the agent uses a tool for Bash, Read, Write, Edit, MultiEdit, mcp__akb__.* and mcp__akb_test__.* tool calls, executing akb_pm_hook.py via python3. From dnotitia/akb.

dnotitia/akb

Settings file Claude Code

Agent settings declaring 4 hook events (SessionStart, UserPromptSubmit, PreToolUse, Stop) and 11 allowed tools.

dnotitia/akb

Instructions file CodexOpenCode

AGENTS.md instructions for dnotitia/akb, covering akb project guide, architecture, frontend design system, 2-layer mcp architecture and deployment.

dnotitia/akb

Instructions file

Claude Code instructions for dnotitia/akb, covering claude guide for akb, mission, default work loop, pm collaboration and docs state machine.

dnotitia/akb

Plugin Claude Code

Bridge Claude Code's session lifecycle into AKB's agent-memory vault.

dnotitia/akb

Plugin Claude Code

Ingest coding sessions into an AKB vault as structured notes.

dnotitia/akb

Skill Claude CodeCodex

Ingest a coding session JSONL into AKB as structured notes — session report + parallel-drafted TIL / task / idea / decision sub-notes. Auto-discovers the current session's JSONL when no positional path is given (Claude / Codex). --delegate {target} fires the work to another target's CLI and exits.

dnotitia/akb

MCP server Claude CodeCodexCursor +2

AKB MCP stdio client — connect any AI agent to AKB knowledge base. Zero dependencies, auto-reconnect. Runs locally from the akb-mcp npm package. Needs 2 environment variables to run.

dnotitia/akb

Agent

Ingest one Confluence page into an AKB vault as a five-section LLM-wiki summary document, fetched live via the Atlassian MCP server.

dnotitia/akb

Agent

Ingest one document (local file or web URL) into an AKB vault as a five-section LLM-wiki summary page, optionally preserving the original bytes in the raw file layer.

dnotitia/akb

Agent

Record one Jira issue as an atlassian-issue document in an AKB vault — title/description/resolution/comments quoted verbatim. Fetched live via the Atlassian MCP server; always upsert.

dnotitia/akb

Skill Claude CodeCodex

Ingest whatever you point at into an AKB vault — a local file, a web URL, a GitHub PR/release/commit, a Confluence page, or a Jira issue. Auto-detects the source type and dispatches to a specialized ingest subagent; the router fetches and writes nothing itself. One target per invocation; globs expand to a sequential…

dnotitia/akb

Skill Claude CodeCodex

Answer a question from the AKB vault — decompose, search (hybrid / graph), ground in compiled-truth-over-timeline precedence, and synthesize a cited answer with gap/conflict/stale flags. Read-only.

dnotitia/akb

MCP server Claude CodeCodexCursor +2

Git-backed org memory for AI agents — hybrid search, tables, files & a URI graph over MCP. Runs locally from the akb-mcp npm package. Needs 2 environment variables to run.

zjunlp/SciAtlas

Skill Claude CodeCodex

Use only the current SciAtlas automated review workflow (reviewpipeline) to take a novice user from zero setup to a final automated review of a research idea or paper, including setup, registration guidance, workflow configuration, retrieval, artifact reading, and synthesis. Trigger when the user asks whether an idea…