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Support the Open Source Projects We Depend On
The skills in this repository depend on open source projects maintained by developers and research communities around the world. This page highlights projects to cite, contribute to, and support; the skill catalog is the complete inventory.
If you find value in these skills, please consider supporting the underlying open source projects that make them possible.
How to Support Open Source
- Star repositories on GitHub - It's free and helps projects gain visibility
- Sponsor maintainers directly through GitHub Sponsors, Open Collective, or project-specific donation pages
- Contribute code, documentation, or bug reports
- Cite projects in your publications
- Share projects with colleagues
Featured Projects by Domain
| Project |
Description |
Links |
| Biopython |
Computational molecular biology toolkit |
GitHub - Contribute |
| Scanpy |
Single-cell analysis in Python |
GitHub - scverse |
| AnnData |
Annotated data matrices for single-cell |
GitHub |
| scvi-tools |
Deep learning for single-cell omics |
GitHub |
| Arboreto |
Gene regulatory network inference |
GitHub |
| pysam |
SAM/BAM/VCF file interface |
GitHub |
| scikit-bio |
Bioinformatics library |
GitHub |
| gget |
Gene and transcript info retrieval |
GitHub |
| deepTools |
Tools for deep-sequencing data |
GitHub |
| geniml |
Machine learning for genomic interval sets |
GitHub |
| Gtars |
Rust/Python genomic interval toolkit |
GitHub |
| ETE Toolkit |
Phylogenetic tree analysis |
GitHub |
| Waypoint |
Microbiome foundation models, taxonomic embeddings, and the Compass benchmark |
GitHub |
| Folklore MCP adapter |
Public protocol adapter for variant evidence, gene-disease assertions, and literature; the hosted interpretation engine is separate |
GitHub |
Scientific Data Management & Knowledge Graphs
| Project |
Description |
Links |
| DataLad |
Dataset retrieval, versioning, and computational provenance |
GitHub |
| git-annex |
Large-file content management used by DataLad |
Project |
| ARAX / RTX |
Biomedical knowledge-graph queries and provenance through NCATS Translator |
GitHub |
| Project |
Description |
Links |
| RDKit |
Cheminformatics toolkit |
GitHub - Cite |
| Datamol |
Molecular manipulation made easy |
GitHub |
| DeepChem |
Deep learning for chemistry |
GitHub |
| TorchDrug |
Drug discovery with PyTorch |
GitHub |
| molfeat |
Molecular featurization |
GitHub |
| MedChem |
Medicinal chemistry filters |
GitHub |
| PyTDC |
Therapeutics Data Commons |
GitHub |
Proteomics & Mass Spectrometry
| Project |
Description |
Links |
| matchms |
Mass spectrometry data processing |
GitHub |
| pyOpenMS |
Mass spectrometry toolkit |
GitHub |
Machine Learning & AI
| Project |
Description |
Links |
| PyTorch Lightning |
Deep learning framework |
GitHub |
| Transformers |
State-of-the-art NLP |
GitHub |
| scikit-learn |
Machine learning in Python |
GitHub - Donate |
| PyTorch Geometric |
Geometric deep learning |
GitHub |
| PyMC |
Probabilistic programming |
GitHub - Donate |
| SHAP |
Model interpretability |
GitHub |
| Stable Baselines3 |
Reinforcement learning |
GitHub |
| PufferLib |
High-performance reinforcement learning environments and training |
GitHub |
| scikit-survival |
Survival analysis |
GitHub |
| aeon |
Time series ML toolkit |
GitHub |
| PyMOO |
Multi-objective optimization |
GitHub |
| UMAP |
Dimensionality reduction |
GitHub |
| HypoGeniC |
LLM-assisted candidate textual hypothesis generation from labeled data |
GitHub |
Data Science & Visualization
| Project |
Description |
Links |
| Matplotlib |
Plotting library |
GitHub - Donate |
| Seaborn |
Statistical visualization |
GitHub |
| Plotly |
Interactive visualizations |
GitHub |
| NetworkX |
Network analysis |
GitHub - Donate |
| SymPy |
Symbolic mathematics |
GitHub - Donate |
| statsmodels |
Statistical modeling |
GitHub |
| GeoPandas |
Geospatial data in Python |
GitHub |
| Polars |
Fast DataFrame library |
GitHub |
| Dask |
Parallel computing |
GitHub - Donate |
| Vaex |
Out-of-core DataFrames |
GitHub |
Medical Imaging & Digital Pathology
| Project |
Description |
Links |
| pydicom |
DICOM file handling |
GitHub |
| histolab |
Digital pathology preprocessing |
GitHub |
| PathML |
Pathology ML toolkit |
GitHub |
| OMERO.py |
Python client for the OMERO microscopy data platform |
GitHub |
Healthcare & Clinical
| Project |
Description |
Links |
| PyHealth |
Healthcare AI toolkit |
GitHub |
| NeuroKit2 |
Neurophysiological signal processing |
GitHub |
Materials Science & Physics
| Project |
Description |
Links |
| Pymatgen |
Materials analysis |
GitHub |
| COBRApy |
Metabolic modeling |
GitHub |
| Astropy |
Astronomy library |
GitHub - Donate |
Quantum Computing
| Project |
Description |
Links |
| Qiskit |
IBM quantum computing SDK |
GitHub |
| Cirq |
Google quantum computing |
GitHub |
| PennyLane |
Quantum ML library |
GitHub |
| QuTiP |
Quantum toolbox in Python |
GitHub |
Simulation & Engineering
| Project |
Description |
Links |
| SimPy |
Discrete-event simulation |
GitLab |
| FluidSim |
CFD framework |
GitHub |
| FluidFFT |
FFT framework and plugins used by FluidSim |
GitHub |
Laboratory & Automation
| Project |
Description |
Links |
| PyLabRobot |
Lab automation control |
GitHub |
Protein Engineering
| Project |
Description |
Links |
| ESM |
Evolutionary scale modeling |
GitHub |
| Project |
Description |
Links |
| Zarr |
Chunked array storage |
GitHub |
| FlowIO |
Flow cytometry I/O |
GitHub |
Scientific Communication & Documents
| Project |
Description |
Links |
| python-pptx |
Create and inspect editable PowerPoint .pptx files |
GitHub |
Many of the projects above are sponsored by NumFOCUS, a nonprofit supporting open source scientific computing. Consider donating to NumFOCUS to support the broader ecosystem.
Projects in this collection listed in the NumFOCUS sponsorship directory (checked 2026-09-13):
- scikit-learn
- Matplotlib
- NetworkX
- SymPy
- Dask
- Astropy
- PyMC
- GeoPandas
- Zarr
- scverse
scverse Ecosystem
The scverse consortium maintains foundational tools for single-cell omics:
- Scanpy
- AnnData
- scvi-tools
- And more
Consider supporting their mission to advance single-cell research.
A Note from K-Dense
At K-Dense, we believe in giving back to the communities that make our work possible. We encourage all users of Scientific Agent Skills to:
- Acknowledge these projects when you use them in research
- Contribute back improvements when you can
- Support maintainers financially if you derive commercial value
The open source scientific Python ecosystem is a shared resource. Let's keep it thriving together.
This list is not exhaustive. Many other excellent open source projects power the skills in this repository. If you notice a project that should be listed here, please open a PR!