Aristotle

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45 repositories

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
•31•244•37•8•Updated Dec 25, 2024Dec 25, 2024
spateo-tutorials
Public
tutorials for spateo package
Jupyter Notebook
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MIT License
•2•16•5•0•Updated Dec 25, 2024Dec 25, 2024
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
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BSD 3-Clause "New" or "Revised" License
•59•430•10•13•Updated Dec 21, 2024Dec 21, 2024
awesome-papers-on-biological-agent-models
Public
This repo collects all latest research on agent system for biological studies
0•10•0•0•Updated Dec 13, 2024Dec 13, 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
•4•15•2•0•Updated Dec 9, 2024Dec 9, 2024
qiu_lab_website
Public
The source code for the Qiu lab website (based on ato-neulab)
HTML
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MIT License
•0•0•8•0•Updated Dec 7, 2024Dec 7, 2024
dynamo-tutorials
Public
Tutorials on using latest dynamo package
dynamo
Jupyter Notebook
•11•24•4•0•Updated Oct 29, 2024Oct 29, 2024
CSP4ML
Public
repo for modeling and analyzing metabolic labeling data
Jupyter Notebook
•0•2•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
spateo-notebooks
Public
Jupyter Notebook
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MIT License
•0•3•2•0•Updated Aug 26, 2024Aug 26, 2024
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
•5•17•4•1•Updated Aug 15, 2023Aug 15, 2023
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
•2.5k•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•39•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
•8•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
•94•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
•34k•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
•93•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
•115•0•0•0•Updated Nov 19, 2020Nov 19, 2020
COVID-19-RNA-Seq-datasets
Public
A repository for sharing information on available COVID-19 RNA-Seq datasets
Python
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MIT License
•23•0•0•0•Updated Nov 11, 2020Nov 11, 2020
mpltex
Public
A python package for producing publication quality images using matplotlib.
Python
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Other
•22•0•0•0•Updated Sep 8, 2020Sep 8, 2020
scNT-seq
Public
Jupyter Notebook
•13•0•0•0•Updated Aug 31, 2020Aug 31, 2020
glmGamPoi
Public
Fit Gamma-Poisson Generalized Linear Models Reliably
R
•15•1•0•0•Updated Aug 24, 2020Aug 24, 2020
vcs
Public
Visualization Control System
Jupyter Notebook
•13•0•0•0•Updated Jul 20, 2020Jul 20, 2020
streamlines
Public
Streamlines calculator
JavaScript
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MIT License
•27•0•0•0•Updated Jul 16, 2020Jul 16, 2020