Grimm Lab - Bioinformatics and Machine Learning

All

33 repositories

permGWAS
Public
Efficient Permutation-based GWAS for Normal and Skewed Phenotypic Distributions
gwas gpu-acceleration permutations linear-mixed-models skewed-data westfall-young
Python
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MIT License
•3•24•1•0•Updated Nov 6, 2024Nov 6, 2024
graphxform
Public
Official code for the paper "GraphXForm: Graph transformer for computer-aided molecular design with application to extraction"
Python
•0•3•0•0•Updated Nov 6, 2024Nov 6, 2024
step-and-reconsider
Public
Variant of gumbeldore for the ECAI paper "Take a Step and Reconsider: Sequence Decoding for Self-Improved Neural Combinatorial Optimization"
Python
•1•7•0•0•Updated Nov 5, 2024Nov 5, 2024
gumbeldore
Public
Official repository for the TMLR paper "Self-Improvement for Neural Combinatorial Optimization: Sample Without Replacement, but Improvement"
Python
•1•17•0•0•Updated Nov 5, 2024Nov 5, 2024
HeliantHome
Public
HeliantHOME: a public and centralized database Home of a comprehensive collection of phenotypes for different Sunflower species
gwas images phenotype population-genetics
Python
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MIT License
•0•1•0•0•Updated Oct 22, 2024Oct 22, 2024
StomaDet
Public
This repository provides the source code of the StomaDetector in "Additive effects of stomata density and leaf ABA levels on maize water use efficiency"
Python
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MIT License
•0•0•0•0•Updated Sep 20, 2024Sep 20, 2024
policy-based-self-competition
Public
Official implementation of the ICLR 2023 paper "Policy-Based Self-Competition for Planning Problems"
gumbel-alphazero
Python
•2•5•0•0•Updated Jul 26, 2024Jul 26, 2024
ProLaTherm
Public
Protein Language Model-based Protein Thermophilicity Prediction
bioinformatics computational-biology protein protein-sequences machine-learning-models
Python
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MIT License
•0•2•0•0•Updated Jun 13, 2024Jun 13, 2024
MicrobiomeBestPracticeReview
Public
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
bioinformatics pipeline best-practices assembly metagenomics microbiome biomedical microbiome-analysis amplicon-sequencing 16s-rrna
Shell
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MIT License
•38•109•0•0•Updated May 12, 2024May 12, 2024
MFWD
Public
Code repository for the manuscript "Manually annotated and curated dataset of diverse weed species in maize and sorghum for computer vision"
Python
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MIT License
•1•7•0•0•Updated Apr 3, 2024Apr 3, 2024
drl4procsyn
Public
Deep reinforcement learning uncovers processes for separating azeotropic mixtures without prior knowledge
Python
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Other
•1•3•0•0•Updated Mar 25, 2024Mar 25, 2024
cem
Public
Convex Envelope Method for determining liquid multi-phase equilibria in systems with arbitrary number of components
Python
•0•2•0•0•Updated Feb 9, 2024Feb 9, 2024
ForeTiS
Public
Time Series Forecasting in Python
time-series-analysis time-series-prediction time-series-forecasting python machine-learning deep-learning
Python
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GNU General Public License v3.0
•0•11•0•0•Updated Oct 18, 2023Oct 18, 2023
easyPheno
Public
easyPheno: a model agnostic phenotype prediction framework
machine-learning deep-learning genomic-selection phenotype-prediction
Python
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GNU General Public License v3.0
•5•10•0•0•Updated Oct 10, 2023Oct 10, 2023
ForeTiS-HortiCo
Public
Python
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MIT License
•0•2•0•0•Updated Sep 5, 2023Sep 5, 2023
DeBlurWeedSeg
Public
Improved weed segmentation in UAV imagery of sorghum fields with a combined deblurring segmentation model
deblurring precision-agriculture smart-farming weed-segmentation deep-learning
Python
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MIT License
•1•2•0•0•Updated Aug 23, 2023Aug 23, 2023
UAVWeedSegmentation
Public
Deep Learning-based Early Weed Segmentation using Motion Blurred UAV Images of Sorghum Fields
precision-agriculture uav-images weed-detection weed-segmentation deep-learning
Python
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MIT License
•3•17•0•0•Updated Jul 24, 2023Jul 24, 2023
GerminationPrediction
Public
Accurate Machine Learning Based Germination Detection, Prediction and Quality Assessment of Different Seed Cultivars
seed-germination germination-detection machine-learning deep-learning object-detection
Python
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MIT License
•4•12•0•0•Updated Jul 24, 2023Jul 24, 2023
SynGameZero
Public
SynGameZero – Flowsheet Synthesis in a Game environment with Zero Knowledge
machine-learning reinforcement-learning hierarchical-reinforcement-learning process-engineering
MIT License
•0•4•0•0•Updated Jul 20, 2023Jul 20, 2023
HorticulturalSalesPredictions
Public
Machine Learning Outperforms Classical Forecasting on Horticultural Sales Predictions
horticulture demand-forecasting sales-forecasting multivariate-time-series-prediction
Python
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MIT License
•5•10•0•0•Updated Oct 26, 2022Oct 26, 2022
phenotype_prediction
Public
A comparison of classical and machine learning-based phenotype prediction methods on simulated data and three plant species
deep-neural-networks blup genomic-selection phenotype-prediction plant-phenotyping arabidopsis-thaliana machine-learning
Jupyter Notebook
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MIT License
•2•2•0•0•Updated Oct 26, 2022Oct 26, 2022
transcriptional-translational-coupling
Public
Systematic analysis of the underlying genomic architecture for transcriptional-translational coupling in prokaryotes
transcriptional-translational bioinformatics
Python
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MIT License
•0•0•0•0•Updated Jul 29, 2022Jul 29, 2022
evars-gpr
Public
EVARS-GPR: EVent-triggered Augmented Refitting of Gaussian Process Regression for Seasonal Data
data-augmentation gaussian-process-regression change-point-detection seasonal-time-series online-time-series-forecasting
Python
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MIT License
•1•2•0•0•Updated Mar 22, 2022Mar 22, 2022
BookChapter-RNA-Seq-Analyses
Public
Best practice RNA-Seq analysis pipeline for reference-based RNA-Seq analysis
bioinformatics pipeline differential-expression rnaseq-analysis
Shell
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GNU General Public License v3.0
•11•39•0•0•Updated May 17, 2021May 17, 2021
AraGWAS
Public
The AraGWAS Catalog - Togninalli*, Seren*, ..., Grimm, 2018, Nucleic Acid Research (https://bit.ly/2DaVj2r)
Vue
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MIT License
•5•1•0•0•Updated Sep 16, 2019Sep 16, 2019
AraPheno
Public
AraPheno: A public database for Arabidopsis thaliana phenotypes. Seren*, Grimm*, et. al. 2017, Nucleic Acid Research (https://bit.ly/2AwpTRF)
HTML
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MIT License
•9•1•0•0•Updated Sep 16, 2019Sep 16, 2019
Lecture_ML4Genomics
Public
Introduction into machine learning and its applications in genomics and genetics
Jupyter Notebook
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GNU General Public License v3.0
•0•1•0•0•Updated Oct 2, 2018Oct 2, 2018
easyGWASCore
Public
Computational Framework for Genome-Wide Association Studies and Meta-Studies in C/C++ with Python Interfaces – Grimm et. al. 2017, Plant Cell (https://bit.ly/2Jqgr5e)
C++
•6•0•0•0•Updated Feb 16, 2018Feb 16, 2018
Structural-Variant-Prediction-SV-M
Public
Structural Variant Machine (SV-M) to accurately predict InDels from NGS paired-end short reads – Grimm*, Hagmann*, et. al. 2013, BMC Genomics (https://bit.ly/2EQOu7X)
C++
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GNU General Public License v3.0
•2•0•0•0•Updated Oct 19, 2016Oct 19, 2016
SConES
Public
A network-guided multi-locus association mapping method (Azencott et al., ISMB/Bioinformatics 2013) http://goo.gl/a8f6az
C++
•2•0•0•0•Updated Oct 19, 2016Oct 19, 2016