MunskyGroup

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35 repositories

FISH_Processing
Public
Repository to automatically process Fluorescence In Situ Hybridization (FISH) images using Cellpose and BIG-FISH (FISH-quant v2).
python fish automation image-processing bioinformatics-pipeline
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•3•14•16•1•Updated Nov 22, 2024Nov 22, 2024
SSIT
Public
Stochastic System Identification Toolkit (SSIT) to model, analyze and design single-cell experiments
matlab modeling markov-chain parameter-estimation bayesian-inference single-cell stochastic-processes experimental-design
MATLAB
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BSD 3-Clause "New" or "Revised" License
•8•2•5•1•Updated Nov 15, 2024Nov 15, 2024
pycro-manager-munsky
Public
A "severed" fork of Pycro-manager v0.23 patched for compatibility with latest versions of NumPy
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Sep 29, 2024Sep 29, 2024
rSNAPsim
Public
RNA Sequence to NAscent Protein simulator
Jupyter Notebook
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MIT License
•1•2•12•1•Updated Aug 27, 2024Aug 27, 2024
rsnaped
Public
A library to quantify and design single-molecule gene expression experiments.
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•2•0•0•Updated Jun 26, 2024Jun 26, 2024
UQbio2024_Team4
Public
Jupyter Notebook
•0•0•0•0•Updated Jun 20, 2024Jun 20, 2024
UQbio2024_Team2
Public
Jupyter Notebook
•0•0•0•0•Updated Jun 18, 2024Jun 18, 2024
UQbio2024_Team6
Public
Jupyter Notebook
•0•0•0•0•Updated Jun 18, 2024Jun 18, 2024
UQbio2024_Team3
Public
Jupyter Notebook
•1•0•0•0•Updated Jun 18, 2024Jun 18, 2024
UQbio2024_Team5
Public
Jupyter Notebook
•0•0•0•0•Updated Jun 17, 2024Jun 17, 2024
UQbio2024_Team1
Public
Jupyter Notebook
•0•0•0•0•Updated Jun 14, 2024Jun 14, 2024
uqbio2024
Public
Repository of codes and notebooks used during the 2024 UQ-Bio Summer School.
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•9•11•0•0•Updated Jun 14, 2024Jun 14, 2024
mlrose
Public
Python package for implementing a number of Machine Learning, Randomized Optimization and SEarch algorithms.
Python
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BSD 3-Clause "New" or "Revised" License
•250•0•0•0•Updated May 7, 2024May 7, 2024
MicroscopyControlAndProcessing
Public
Python
•0•0•2•0•Updated Mar 20, 2024Mar 20, 2024
thompson_etal_plos_one_2019
Public
Jupyter Notebook
•1•3•0•3•Updated Jul 6, 2023Jul 6, 2023
UQBio2023
Public
3rd Annual Undergraduate Quantitative Biology (UQ-bio) Summer School
statistics image-processing drug-discovery stochastic-models machine-learning
Python
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BSD 3-Clause "New" or "Revised" License
•2•12•0•0•Updated Jun 21, 2023Jun 21, 2023
Vo_et_al_2023_Matlab
Public
Matlab codes for analyzing and designing single-cell experiments.
uncertainty-quantification fisher-information-matrix model-identification single-cell-experiment chemical-master-equation finite-state-projection
MATLAB
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated May 3, 2023May 3, 2023
Multiplexing_project
Public
Jupyter Notebook
•0•2•0•0•Updated May 2, 2023May 2, 2023
Albright_et_al_2019
Public
Jupyter Notebook
•0•0•0•0•Updated Mar 27, 2023Mar 27, 2023
uqbio2022
Public
2nd Annual Undergraduate Quantitative Biology (UQ-bio) Summer School
5•16•0•0•Updated Jun 14, 2022Jun 14, 2022
Forero_2020
Public
Mathematica
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Creative Commons Attribution 4.0 International
•0•0•0•0•Updated May 27, 2022May 27, 2022
uqbio2021
Public
This is the repository for the 2021 uq-bio Summer School
Jupyter Notebook
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MIT License
•6•12•0•0•Updated May 9, 2022May 9, 2022
Matlab_Wrap_for_JHU_COVID19
Public
MATLAB
•5•3•2•0•Updated Jan 4, 2022Jan 4, 2022
Kalb_Vo_2021
Public
Jupyter Notebook
•1•0•0•0•Updated Jul 28, 2021Jul 28, 2021
Kroeger_et_al_2021
Public
Jupyter Notebook
•0•0•0•0•Updated Jun 15, 2021Jun 15, 2021
Koch_Aguilera_etal_2020
Public
MATLAB
•0•0•0•0•Updated Jul 16, 2020Jul 16, 2020
Fox_Complexity_2020
Public
MATLAB
•1•0•1•0•Updated Jun 17, 2020Jun 17, 2020
Munsky_et_al_2018
Public
MATLAB
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GNU General Public License v3.0
•0•0•0•0•Updated Sep 23, 2019Sep 23, 2019
Aguilera_PLoS_CompBio_2019
Public
JavaScript
•0•0•0•0•Updated Sep 17, 2019Sep 17, 2019
Tanhaemami_Phys_Biol_2019
Public
MATLAB
•0•0•0•0•Updated Aug 3, 2019Aug 3, 2019