Plant-Food-Research-Open

All

12 repositories

assemblyqc
Public
A Nextflow pipeline for evaluating assembly quality
quality-control statistics genome taxonomy assembly repeat hi-c report k-mer synteny
Nextflow
•
MIT License
•7•36•58•1•Updated Jul 24, 2025Jul 24, 2025
TEgenomeSimulator
Public
TEgenomeSimulator: A tool to simulate TE mutation and insertion into a random-synthesised or user-provided genome.
Python
•
GNU General Public License v3.0
•2•3•1•0•Updated Jul 22, 2025Jul 22, 2025
calisim-examples-workshop-material
Public
Jupyter Notebook
•
Apache License 2.0
•1•1•5•11•Updated Jul 21, 2025Jul 21, 2025
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
•
Apache License 2.0
•0•2•2•11•Updated Jul 16, 2025Jul 16, 2025
pfram
Public
shiny h2o tidyverse bayesian-inference stan plumber causal-inference automl tidymodels
R
•
Apache License 2.0
•0•1•14•0•Updated Jul 10, 2025Jul 10, 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
•
Apache License 2.0
•2•15•9•5•Updated Jul 1, 2025Jul 1, 2025
genepal
Public
A Nextflow pipeline for genome and pan-genome annotation
gene annotation genome phased pangenome
Nextflow
•
MIT License
•7•14•37•2•Updated Jun 24, 2025Jun 24, 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
•
MIT License
•0•0•0•0•Updated Apr 9, 2025Apr 9, 2025
moiraine
Public
An R package to construct Multi-Omics Integration Reproducible Analyses in R.
R
•
Other
•1•7•0•0•Updated Jan 22, 2025Jan 22, 2025
moiraine-manual
Public
User manual for the moiraine R package
R
•
MIT License
•0•0•0•0•Updated Aug 11, 2024Aug 11, 2024
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
•
GNU General Public License v3.0
•4•2•2•0•Updated Jul 16, 2024Jul 16, 2024
HEImiRA-pipeline
Public
Host Environment Intersection miRNA Annotation pipeline
Nextflow
•
GNU General Public License v3.0
•0•0•0•0•Updated Jun 19, 2023Jun 19, 2023