cellRAG
This file will become your README and also the index of your
documentation.
Developer Guide
If you are new to using nbdev here are some useful pointers to get you
started.
Install cellRAG in Development mode
# Install uv
curl -LsSf https://astral.sh/uv/install.sh | sh
# Create and activate a virtual environment
uv venv
source .venv/bin/activate
# Install the project in editable mode
uv pip install -e ".[dev]"
# Install additional dependencies
uv pip install nbdev jupyter
Usage
Installation
Install latest from the GitHub
repository:
$ pip install git+https://github.com/LA3D/cellRAG.git
Documentation
Documentation can be found hosted on this GitHub
repository’s
pages. Additionally you can find
package manager specific guidelines on
conda and
pypi respectively.
How to use
Fill me in please! Don’t forget code examples:
References
-
Stephen, S., Faulk, M., Janowicz, K., Fisher, C., Thelen, T., Zhu,
R., Hitzler, P., Shimizu, C., Currier, K., Schildhauer, M., Rehberger,
D., Wang, Z., & Christou, A. (2024). The S2 hierarchical discrete
global grid as a nexus for data representation, integration, and
querying across geospatial Knowledge Graphs. In arXiv [cs.AI].
arXiv.
-
Edge, D., Trinh, H., Cheng, N., Bradley, J., Chao, A., Mody, A.,
Truitt, S., Metropolitansky, D., Ness, R. O., & Larson, J. (2024).
From local to global: A graph RAG approach to query-focused
summarization. In arXiv [cs.CL].
arXiv.
-
Guo, Z., Xia, L., Yu, Y., Ao, T., & Huang, C. (2024). LightRAG:
Simple and fast retrieval-Augmented Generation. In arXiv [cs.IR].
arXiv.
-
KARMA: Leveraging Multi-Agent LLMs for Automated Knowledge Graph
Enrichment. (n.d.). Retrieved February 26,
2025,
-
Buehler, M. J. (2025). Agentic deep graph reasoning yields
self-organizing knowledge networks. In arXiv [cs.AI].
arXiv.
-
Lu, P., Chen, B., Liu, S., Thapa, R., Boen, J., & Zou, J. (2025).
OctoTools: An agentic framework with extensible tools for complex
reasoning. In arXiv [cs.LG]. arXiv.
http://arxiv.org/abs/2502.11271
-
Li, J., Lai, Y., Li, W., Ren, J., Zhang, M., Kang, X., Wang, S., Li,
P., Zhang, Y.-Q., Ma, W., & Liu, Y. (2024). Agent Hospital: A
simulacrum of hospital with evolvable medical agents. In arXiv
[cs.AI]. arXiv.
http://arxiv.org/abs/2405.02957