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.
INTERACTIVE DASHBOARD to explore the Belly Button Biodiversity datasetLinks to an external site., which catalogs the microbes that colonize human navels.
Nextflow pipeline for pathogen surveillance in wastewater
A tool for phylogenetic comparison and analysis of microbe including gene's environmental association
Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.
A roguelike game where you play a micro organism inside a larger organism!
Omero based integrated Workflow for annotating Microbes in the Cloud
DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further in…
A theorectical investigation into mechanisms of drought legacy formation and influencing factors in soil microbiomes using DEMENTpy.
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.
Microbe-Metabolite INteractions-based metabolic profiles Predictor
A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism
To explore biotic associations of microbes at the community level. See the detailed package tutorial (https://joshualiuxu.github.io/).
Deep learning-based instance segmentation tool for roundish objects in 2D and 2D+t data
Significance of non-microbial processes in organic matter decompositon in ecosystems across scales
Classification model predicting the type of microbe from provided features
This repository contains python code used to create figures in the accompanying manuscript.
Classification of stressful microbial growth conditions using gene fitness data and support vector machines
Neutral evolution modeling of microbes.
Interactive dashboard to explore the Belly Button Biodiversity dataset using Plotly for Javascript.
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