Graphs that teach > graphs that impress. Turn any code into an interactive knowledge graph you can explore, search, and ask questions about. Works with Claude Code, Codex, Cursor, Copilot, Gemini CLI, and more.
Pre-indexed code knowledge graph, auto syncs on code changes, for Claude Code, Codex, Gemini, Cursor, OpenCode, AntiGravity, Kiro, and Hermes Agent — fewer tokens, fewer tool calls, 100% local
npx @colbymchenry/codegraphA hand-picked collection of the finest of resources for the most awesome of agents, Claude Code, the undisputed champion of coding companions, from the unstoppable team at Anthropic PBC. A delectable showcase of top tier skills, ambidextrous agents, scintillating status lines, top notch developer tooling, and also we have plugins
1663 GitHub stars recorded
Download the latest build from GitHub Releases.
ClaudePrism integrates uv — the fast Python package manager — directly into the app. One click to install uv, one click to create a project-level virtual environment. Claude Code automatically uses the .venv when running Python code, so you can generate plots, run analysis scripts, and process data without leaving the editor.
Browse and install domain-specific skills from K-Dense Scientific Skills — curated prompts and tool configurations that give Claude deep knowledge in specialized fields:
| Domain | Skills |
|---|---|
| Bioinformatics & Genomics | Scanpy, BioPython, PyDESeq2, PySAM, gget, AnnData, ... |
| Cheminformatics & Drug Discovery | RDKit, DeepChem, DiffDock, PubChem, ChEMBL, ... |
| Data Analysis & Visualization | Matplotlib, Seaborn, Plotly, Polars, scikit-learn, ... |
| Machine Learning & AI | PyTorch Lightning, Transformers, SHAP, UMAP, PyMC, ... |
| Clinical Research | ClinicalTrials.gov, ClinVar, DrugBank, FDA, ... |
| Scientific Communication | Literature Review, Grant Writing, Citation Management, ... |
| Multi-omics & Systems Biology | scvi-tools, COBRApy, Reactome, Bioservices, ... |
| And more | Materials Science, Lab Automation, Proteomics, Physics, ... |
Skills are installed globally (~/.claude/skills/) or per-project, and Claude automatically loads them when relevant.
Pick a template (paper, thesis, presentation, poster, letter, etc.), give it a name, optionally describe what you're writing — ClaudePrism sets up the project and generates initial content with AI. Drag & drop reference files (PDF, BIB, images) and start writing immediately.
Chat with Claude directly in the editor. Select between Sonnet, Opus, Haiku models with adjustable reasoning effort levels. Persistent sessions, tool use (file edit, bash, search), and extensible slash commands.
Every save creates a snapshot in a local Git repository (.claudeprism/history.git/). Label important checkpoints, browse diffs between any two snapshots, and restore previous versions. When Claude suggests edits, changes appear in a dedicated panel with visual diffs — accept or reject per chunk, or apply/undo all at once (⌘Y / ⌘N).
Tectonic is embedded directly in the app. Packages are downloaded once on first use and cached locally. After that, compilation works fully offline with no TeX Live installation required.
Press ⌘X to enter capture mode, drag to select any region in the PDF — the captured image is pinned to the chat composer so you can immediately ask Claude about it. Great for asking about equations, figures, tables, or reviewer comments.
Native MuPDF rendering with SyncTeX support — click a position in the PDF to jump to the corresponding source line. Supports zoom, text selection, and capture.
CodeMirror 6 with LaTeX/BibTeX syntax highlighting, real-time error linting, find & replace (regex), and multi-file project support with auto-save.
/review, /init) + custom commands from .claude/commands/.