aristoteleo repositories

62 repositories

PantheonOS
Public
A general, evolvable, and distributed agent framework & harness for data science.
agent data-science bioinformatics
agent data-science bioinformatics ai biology harness claw ai-agents singlecell spatial-transcriptomics
Python
•
BSD 2-Clause "Simplified" License
•67•487•17•8•Updated Oct 5, 2026Oct 5, 2026
veckit
Public
Virtual Embryo Challenge (VEC) local scorer: score a submitted .h5ad against the T1/T2/T3 metric panels, offline, against reference files you supply.
Python
•
MIT License
•6•15•3•5•Updated Oct 2, 2026Oct 2, 2026
qiu_lab_website
Public
The source code for the Qiu lab website (based on ato-neulab)
HTML
•
MIT License
•0•0•12•0•Updated Oct 1, 2026Oct 1, 2026
tabula-reproducibility
Public
The repo that reproduces figures in the tabula paper
Python
•1•0•0•0•Updated Aug 10, 2026Aug 10, 2026
tabula
Public
Single cell foundation model with federated tabular learning
singlecell virtual-cell foundation-model
singlecell virtual-cell foundation-model
Jupyter Notebook
•
Other
•5•40•1•0•Updated Aug 10, 2026Aug 10, 2026
virtual_cell
Public
the website that will be initially used for the scFM review
MIT License
•0•0•0•0•Updated Jul 29, 2026Jul 29, 2026
dynamo-release
Public
Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geomet…
dynamo scrna-seq differential-geometry
dynamo scrna-seq differential-geometry dynamical-systems vector-field scslam-seq potential-landscape nasc-seq sci-fate scnt-seq
Python
•
BSD 3-Clause "New" or "Revised" License
•60•510•0•2•Updated Jul 26, 2026Jul 26, 2026
epione
Public
Analysis of epigenetic data in Python
atac scatac-seq
atac scatac-seq
Jupyter Notebook
•
GNU General Public License v3.0
•1•11•1•1•Updated Jul 21, 2026Jul 21, 2026
dynamo-tutorials
Public
Tutorials on using latest dynamo package
dynamo
dynamo
Jupyter Notebook
•14•27•3•0•Updated Jul 1, 2026Jul 1, 2026
chiron
Public
TypeScript
•
Other
•0•3•0•0•Updated Jun 30, 2026Jun 30, 2026
Navigo-release
Public
Package for the Navigo project: Generative Modeling of Mouse Embryogenesis for Fate and Disease Prediction
Python
•
BSD 2-Clause "Simplified" License
•4•18•0•0•Updated Jun 10, 2026Jun 10, 2026
awesome-agent-function
Public
Python
•0•0•0•0•Updated Jun 5, 2026Jun 5, 2026
chiron-platform
Public
Chiron Platform is a decentralized federated training platform for single-cell foundation models, built to train and orchestrate Tabula across distributed BioEn…
TypeScript
•1•0•0•0•Updated May 27, 2026May 27, 2026
pantheonos-reproducibility
Public
Reproducibility repo for PantheonOS paper
Python
•
BSD 2-Clause "Simplified" License
•0•2•0•0•Updated May 18, 2026May 18, 2026
awesome-llm-evolution
Public
BSD 2-Clause "Simplified" License
•0•2•0•0•Updated Apr 10, 2026Apr 10, 2026
Navigo-docs
Public
Jupyter Notebook
•0•0•0•0•Updated Apr 7, 2026Apr 7, 2026
awesome-skill-generate
Public
Python
•
BSD 2-Clause "Simplified" License
•0•11•0•0•Updated Mar 20, 2026Mar 20, 2026
spateo-release
Public
Spatiotemporal modeling of spatial transcriptomics
spatiotemporal 3d-reconstruction cell-segmentation
spatiotemporal 3d-reconstruction cell-segmentation spatial-transcriptomics
Python
•
BSD 2-Clause "Simplified" License
•45•344•1•12•Updated Feb 25, 2026Feb 25, 2026
awesome-bioagent-papers
Public
Agent self-driven repository on bio-agent papers, i.e. papers on LLM-based agents in biology and medicine.
Python
•9•110•3•31•Updated Feb 10, 2026Feb 10, 2026
pantheon-cli-tutorial
Public
Vue
•1•0•0•0•Updated Aug 25, 2025Aug 25, 2025
dynast-release
Public
Inclusive and efficient quantification of labeling and splicing RNAs for time-resolved metabolic labeling based scRNA-seq experiments
scrna-seq vector-field scslam-seq
scrna-seq vector-field scslam-seq nasc-seq sci-fate scnt-seq rna-velocity metabolic-labeling
Python
•
MIT License
•6•19•4•1•Updated Aug 12, 2025Aug 12, 2025
pantheon-llm
Public
Jupyter Notebook
•0•0•0•0•Updated Aug 6, 2025Aug 6, 2025
Human_Heart_MERFISH_Analysis_2024
Public
MIT License
•0•0•0•0•Updated Jul 17, 2025Jul 17, 2025
spateo-notebooks
Public
Jupyter Notebook
•
MIT License
•0•7•3•0•Updated Mar 6, 2025Mar 6, 2025
spateo-tutorials
Public
tutorials for spateo package
Jupyter Notebook
•
MIT License
•3•21•7•1•Updated Dec 25, 2024Dec 25, 2024
spateo-viewer
Public
Web application demonstrating 3D modeling of spatial transcriptomics
3d-reconstruction spatial-transcriptomics spateo
3d-reconstruction spatial-transcriptomics spateo
Python
•
BSD 2-Clause "Simplified" License
•7•24•5•0•Updated Dec 9, 2024Dec 9, 2024
CSP4ML
Public
repo for modeling and analyzing metabolic labeling data
Jupyter Notebook
•0•9•0•0•Updated Oct 6, 2024Oct 6, 2024
dynamo_readthedocs
Public
deposit tutorials for dynamo readthedocs pages
Python
•
BSD 3-Clause "New" or "Revised" License
•6•0•0•0•Updated Sep 19, 2024Sep 19, 2024
cookiecutter-data-science
Public template
A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.
Python
•
MIT License
•2.6k•0•0•0•Updated Mar 24, 2023Mar 24, 2023
Scribe-py
Public
Regulatory networks with Direct Information in python
network velocity rnaseq
network velocity rnaseq causality singlecell slam-seq
Python
•
BSD 3-Clause "New" or "Revised" License
•7•42•3•1•Updated Mar 9, 2023Mar 9, 2023

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Aristotle

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62 repositories

PantheonOS

veckit

qiu_lab_website

tabula-reproducibility

tabula

virtual_cell

dynamo-release

epione

dynamo-tutorials

chiron

Navigo-release

awesome-agent-function

chiron-platform

pantheonos-reproducibility

awesome-llm-evolution

Navigo-docs

awesome-skill-generate

spateo-release

awesome-bioagent-papers

pantheon-cli-tutorial

dynast-release

pantheon-llm

Human_Heart_MERFISH_Analysis_2024

spateo-notebooks

spateo-tutorials

spateo-viewer

CSP4ML

dynamo_readthedocs

cookiecutter-data-science

Scribe-py

Repositories list

62 repositories