Aristotle

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51 repositories

awesome-bioagent-papers
Public
Agent self-driven repository on bio-agent papers, i.e. papers on LLM-based agents in biology and medicine.
Python
•6•76•2•30•Updated Oct 19, 2025Oct 19, 2025
spateo-release
Public
Spatiotemporal modeling of spatial transcriptomics
spatiotemporal 3d-reconstruction cell-segmentation spatial-transcriptomics
Python
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BSD 2-Clause "Simplified" License
•42•318•20•11•Updated Oct 14, 2025Oct 14, 2025
dynamo-release
Public
Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
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
•63•472•4•15•Updated Oct 13, 2025Oct 13, 2025
pantheon-cli
Public
Pantheon-CLI, our first release of PantheonOS, the AgentOS that re-imagines Science
agent cli singlecell spatial-transcriptomics agentos pantheonos
Python
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Other
•18•209•8•0•Updated Oct 2, 2025Oct 2, 2025
epione
Public
Analysis of epigenetic data in Python
atac scatac-seq
Jupyter Notebook
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GNU General Public License v3.0
•1•7•1•0•Updated Sep 23, 2025Sep 23, 2025
qiu_lab_website
Public
The source code for the Qiu lab website (based on ato-neulab)
HTML
•
MIT License
•0•0•12•0•Updated Sep 20, 2025Sep 20, 2025
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 nasc-seq sci-fate scnt-seq rna-velocity metabolic-labeling
Python
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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
dynamo-tutorials
Public
Tutorials on using latest dynamo package
dynamo
Jupyter Notebook
•13•24•3•0•Updated Jul 30, 2025Jul 30, 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•6•3•0•Updated Mar 6, 2025Mar 6, 2025
tabula
Public
federated learning with tabular learning
Jupyter Notebook
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Other
•2•22•0•1•Updated Mar 4, 2025Mar 4, 2025
spateo-tutorials
Public
tutorials for spateo package
Jupyter Notebook
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MIT License
•3•20•7•0•Updated Dec 25, 2024Dec 25, 2024
spateo-viewer
Public
Web application demonstrating 3D modeling of spatial transcriptomics
3d-reconstruction spatial-transcriptomics spateo
Python
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BSD 2-Clause "Simplified" License
•7•22•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
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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
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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 causality singlecell slam-seq
Python
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BSD 3-Clause "New" or "Revised" License
•7•40•3•1•Updated Mar 9, 2023Mar 9, 2023
logging
Public
Repository for dynamo style's logging functionalities
Python
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MIT License
•0•1•0•0•Updated May 10, 2022May 10, 2022
.github
Public
0•0•0•0•Updated Apr 23, 2022Apr 23, 2022
dynamo-notebooks
Public
Tutorials of Dynamo usage cases and code to reproduce the manuscript
velocity protein dynamo scrna-seq rna notebooks vector-field scslam-seq potential-landscape
Jupyter Notebook
•5•7•0•0•Updated Apr 6, 2022Apr 6, 2022
stereo-seq-with-dynamo
Public
notebooks that use dynamo to analyze the Stereo-seq datasets
Jupyter Notebook
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MIT License
•1•3•0•0•Updated Feb 21, 2022Feb 21, 2022
PISA
Public
A collection of tools to process single-cell omics datasets.
C
•10•0•0•0•Updated Dec 9, 2021Dec 9, 2021
scg_lib_structs
Public
Collections of library structure and sequence of popular single cell genomic methods
HTML
•101•0•0•0•Updated Mar 24, 2021Mar 24, 2021
bebi103
Public
Utilities for BE/Bi 103
Python
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BSD 3-Clause "New" or "Revised" License
•15•0•0•0•Updated Mar 6, 2021Mar 6, 2021
dynamo_submission
Public
notebooks for generating figures for submitting dynamo
Jupyter Notebook
•0•0•0•0•Updated Feb 25, 2021Feb 25, 2021
public-apis
Public
A collective list of free APIs for use in software and web development.
Python
•39k•0•0•0•Updated Jan 1, 2021Jan 1, 2021
DnaFeaturesViewer
Public
👁️ Python library to plot DNA sequence features (e.g. from Genbank files)
Python
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MIT License
•102•0•0•0•Updated Dec 1, 2020Dec 1, 2020
pyGenomeTracks
Public
python module to plot beautiful and highly customizable genome browser tracks
Python
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GNU General Public License v3.0
•123•0•0•0•Updated Nov 19, 2020Nov 19, 2020