Machine Learning for Genomics

All

13 repositories

chrombpnet
Public
Templates for running official ChromBPNet repository pipelines using SLURM scheduler
Jupyter Notebook
•0•0•0•0•Updated May 30, 2025May 30, 2025
SeqPro
Public
Genomic sequence preprocessing toolkit
data-science machine-learning bioinformatics regulatory-genomics python
Python
•
MIT License
•1•12•0•0•Updated May 24, 2025May 24, 2025
tutorials
Public
A set of tutorials for how to use all the tools in ML4GLand
machine-learning regulatory-genomics tutorial
Jupyter Notebook
•0•3•1•0•Updated Feb 6, 2025Feb 6, 2025
SeqData
Public
Annotated sequence data
data-science bioinformatics python machine-learning
Jupyter Notebook
•
MIT License
•1•11•5•2•Updated Feb 2, 2025Feb 2, 2025
EUGENe
Public
Elucidating the Utility of Genomic Elements with Neural Nets
bioinformatics genomics regulatory-genomics python machine-learning deep-learning
Jupyter Notebook
•
MIT License
•6•69•8•1•Updated Dec 2, 2024Dec 2, 2024
SeqDatasets
Public
Datasets for benchmarking, testing and developing in EUGENe
python regulatory-genomics machine-learning datasets
Python
•
MIT License
•0•1•0•0•Updated Dec 2, 2024Dec 2, 2024
SeqExplainer
Public
Interpreting sequence-to-function machine learning models
bioinformatics interpretable-machine-learning regulatory-genomics python machine-learning deep-learning
Jupyter Notebook
•
MIT License
•1•4•0•0•Updated Jan 25, 2024Jan 25, 2024
use_cases
Public
Repository documenting applications of the ML4GLand suite on published datasets
bioinformatics use-cases regulatory-genomics machine-learning
Jupyter Notebook
•0•1•0•0•Updated Jan 3, 2024Jan 3, 2024
.github
Public
0•0•0•0•Updated Nov 9, 2023Nov 9, 2023
EUGENe_paper
Public
Code for generating the figures and results presented in the manuscript EUGENe: A Python toolkit for sequence activity prediction and analysis
Jupyter Notebook
•
Creative Commons Zero v1.0 Universal
•0•4•0•0•Updated Sep 18, 2023Sep 18, 2023
MotifData
Public
Motif representation and analysis toolkit in Python
python bioinformatics regulatory-genomics machine-learning
Jupyter Notebook
•
MIT License
•1•0•0•1•Updated Jul 21, 2023Jul 21, 2023
external
Public
Code snippets and wrappers for use of external tools without forking repos
Jupyter Notebook
•0•0•0•0•Updated Jul 17, 2023Jul 17, 2023
awesome-dl4g
Public
(Soon to be) community-curated list of software packages and data resources for deep learning for genomics (DL4G)
MIT License
•0•2•0•0•Updated Feb 2, 2023Feb 2, 2023