Aristotle

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45 repositories

awesome-papers-on-biological-agent-models
Public
This repo collects all latest research on agent system for biological studies
0•6•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
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•231•37•8•Updated Dec 3, 2024Dec 3, 2024
spateo-tutorials
Public
tutorials for spateo package
Jupyter Notebook
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MIT License
•2•15•5•0•Updated Dec 3, 2024Dec 3, 2024
dynamo-tutorials
Public
Tutorials on using latest dynamo package
dynamo
Jupyter Notebook
•11•24•4•0•Updated Oct 29, 2024Oct 29, 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•428•7•14•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
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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•0•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
•4•16•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
•92•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