A roguelike game where you play a micro organism inside a larger organism!
Microbe-Metabolite INteractions-based metabolic profiles Predictor
This is the code repository for CLM-Microbe model.
A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism
Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.
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…
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
Nextflow pipeline for pathogen surveillance in wastewater
Microbial Culture Media Knowledge Graph - Comprehensive collection of 10,000+ culture media recipes from major international repositories with LinkML schema, ontology grounding, and browser-based exploration
Omero based integrated Workflow for annotating Microbes in the Cloud
Neutral evolution modeling of microbes.
A theorectical investigation into mechanisms of drought legacy formation and influencing factors in soil microbiomes using DEMENTpy.
A phylogenetically-aware framework for detecting evolutionary associations between binary traits
Targeted Probe Design Pipeline. Using mWGS genome bin clusters, prokka annotation predictions, and blast+ databases for generation, processing and filtering probe sequences.
Microbial Community Mechanisms Knowledge Base - LinkML-based modeling of microbial communities with evidence-based ecological interactions
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
A Snakemake workflow for the post-processing of microbial genome assemblies.
Add a description, image, and links to the microbes topic page so that developers can more easily learn about it.
To associate your repository with the microbes topic, visit your repo's landing page and select "manage topics."