This is the code repository for CLM-Microbe model.
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Updated
Jun 14, 2024 - Fortran
This is the code repository for CLM-Microbe model.
To explore biotic associations of microbes at the community level. See the detailed package tutorial (https://joshualiuxu.github.io/).
Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.
Microbe-Metabolite INteractions-based metabolic profiles Predictor
A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism
A roguelike game where you play a micro organism inside a larger organism!
Omero based integrated Workflow for annotating Microbes in the Cloud
Targeted Probe Design Pipeline. Using mWGS genome bin clusters, prokka annotation predictions, and blast+ databases for generation, processing and filtering probe sequences.
Interactive dashboard to explore the Belly Button Biodiversity dataset using Plotly for Javascript.
Targeted Probe Design Pipeline. Using mWGS genome bin clusters, prokka annotation predictions, and blast+ databases for generation, processing and filtering probe sequences.
Neutral evolution modeling of microbes.
Deep learning-based instance segmentation tool for roundish objects in 2D and 2D+t data
INTERACTIVE DASHBOARD to explore the Belly Button Biodiversity datasetLinks to an external site., which catalogs the microbes that colonize human navels.
Python simulation for visualizing the net geochemical outcomes of microbial metabolism - referred to here as "dead-end states." Poster presentation at Univ. Oregon Undergrad Symposium 2022.
A tool for phylogenetic comparison and analysis of microbe including gene's environmental association
Build an interactive dashboard to explore the Belly Button Biodiversity dataset, which catalogues the microbes that colonize human navels by using Plotly and D3.js libraries.
Javascript and D3 are used to create an interactive dashboard to explore a microbes on human subjects dataset.
A theorectical investigation into mechanisms of drought legacy formation and influencing factors in soil microbiomes using DEMENTpy.
This repository contains python code used to create figures in the accompanying manuscript.
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