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.

A tool for phylogenetic comparison and analysis of microbe including gene's environmental association

Javascript and D3 are used to create an interactive dashboard to explore a microbes on human subjects dataset.

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

Using Plotly, JavaScript, d3, and Bootstrap, created an interactive dashboard to explore the Belly Button Biodiversity dataset, which catalogs the microbes that colonize human navels. The dataset reveals that a small handful of microbial species (also called operational taxonomic units, or OTUs, in the study) were present in more than 70% of peo…

Interactive dashboard to explore the Belly Button Biodiversity dataset using Plotly for Javascript.

Significance of non-microbial processes in organic matter decompositon in ecosystems across scales

Classification model predicting the type of microbe from provided features

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.

Targeted Probe Design Pipeline. Using mWGS genome bin clusters, prokka annotation predictions, and blast+ databases for generation, processing and filtering probe sequences.

A theorectical investigation into mechanisms of drought legacy formation and influencing factors in soil microbiomes using DEMENTpy.

Neutral evolution modeling of microbes.

Omero based integrated Workflow for annotating Microbes in the Cloud

Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.

Nextflow pipeline for pathogen surveillance in wastewater

Deep learning-based instance segmentation tool for roundish objects in 2D and 2D+t data

To explore biotic associations of microbes at the community level. See the detailed package tutorial (https://joshualiuxu.github.io/).