A roguelike game where you play a micro organism inside a larger organism!
Microbe-Metabolite INteractions-based metabolic profiles Predictor
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…
Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.
To explore biotic associations of microbes at the community level. See the detailed package tutorial (https://joshualiuxu.github.io/).
This is the code repository for CLM-Microbe model.
A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism
Deep learning-based instance segmentation tool for roundish objects in 2D and 2D+t data
Nextflow pipeline for pathogen surveillance in wastewater
Omero based integrated Workflow for annotating Microbes in the Cloud
A theorectical investigation into mechanisms of drought legacy formation and influencing factors in soil microbiomes using DEMENTpy.
Neutral evolution modeling of microbes.
Targeted Probe Design Pipeline. Using mWGS genome bin clusters, prokka annotation predictions, and blast+ databases for generation, processing and filtering probe sequences.
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.
Targeted Probe Design Pipeline. Using mWGS genome bin clusters, prokka annotation predictions, and blast+ databases for generation, processing and filtering probe sequences.
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.
INTERACTIVE DASHBOARD to explore the Belly Button Biodiversity datasetLinks to an external site., which catalogs the microbes that colonize human navels.
Javascript and D3 are used to create an interactive dashboard to explore a microbes on human subjects dataset.
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