Plant-Food-Research-Open

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13 repositories

r-pipeline-development-workshop
Public
Workshop on pipeline development and model deployment onto Kubernetes via Docker using R.
statistics h2o tidyverse r-language bayesian-inference stan brms causal-inference r-programming statistical-models
HTML
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Apache License 2.0
•1•2•0•10•Updated Oct 7, 2025Oct 7, 2025
calisim-examples-workshop-material
Public
Workshop for calisim: A toolbox for the calibration and evaluation of simulation models.
evolutionary-algorithms abc bayesian-inference uncertainty-quantification sensitivity-analysis bayesian-statistics active-learning sbi approximate-bayesian-computation surrogate-models
Jupyter Notebook
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Apache License 2.0
•1•2•2•10•Updated Oct 5, 2025Oct 5, 2025
calisim
Public
A toolbox for the calibration and evaluation of simulation models.
evolutionary-algorithms abc model-calibration uncertainty-quantification sensitivity-analysis bayesian-optimization active-learning optimisation uncertainty-analysis experimental-design
Python
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Apache License 2.0
•2•15•9•5•Updated Oct 1, 2025Oct 1, 2025
moiraine_publication_code
Public
Code to reproduce the results presented in Angelin-Bonnet et al, 2025 "moiraine: an R package to construct reproducible pipelines for the application and comparison of multi-omics integration methods".
R
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MIT License
•0•0•0•0•Updated Sep 26, 2025Sep 26, 2025
assemblyqc
Public
A Nextflow pipeline for evaluating assembly quality
quality-control statistics genome taxonomy assembly repeat hi-c report k-mer synteny
Nextflow
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MIT License
•8•37•19•0•Updated Sep 23, 2025Sep 23, 2025
moiraine
Public
An R package to construct Multi-Omics Integration Reproducible Analyses in R.
R
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Other
•3•8•1•0•Updated Sep 22, 2025Sep 22, 2025
TEgenomeSimulator
Public
TEgenomeSimulator: A tool to simulate TE mutation and insertion into a random-synthesised or user-provided genome.
HTML
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GNU General Public License v3.0
•2•4•2•1•Updated Sep 9, 2025Sep 9, 2025
FieldNBalance
Public
Nitrogen balance model components and test procedures
python dotnet crop-model mechanistic-models crop-modeling biophysical-modeling mechanistic-modeling nitrogen-balance
Jupyter Notebook
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GNU General Public License v3.0
•4•2•2•0•Updated Aug 22, 2025Aug 22, 2025
Australian_TeaTree_Genomes
Public
Australian Tea Tree Genome
Shell
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MIT License
•0•0•0•0•Updated Jul 24, 2025Jul 24, 2025
pfram
Public
shiny h2o tidyverse bayesian-inference stan plumber causal-inference automl tidymodels
R
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Apache License 2.0
•0•1•14•0•Updated Jul 10, 2025Jul 10, 2025
genepal
Public
A Nextflow pipeline for genome and pan-genome annotation
gene annotation genome phased pangenome
Nextflow
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MIT License
•7•15•37•2•Updated Jun 24, 2025Jun 24, 2025
moiraine-manual
Public
User manual for the moiraine R package
R
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MIT License
•0•0•0•0•Updated Aug 11, 2024Aug 11, 2024
HEImiRA-pipeline
Public
Host Environment Intersection miRNA Annotation pipeline
Nextflow
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GNU General Public License v3.0
•0•0•0•0•Updated Jun 19, 2023Jun 19, 2023