ecoli

EcoliTyper: A species-optimized computational pipeline for comprehensive genotyping and surveillance of Escherichia coli. Perfect for clinical microbiology, outbreak investigations, and genomic research.

Toronto's open source beach app

E. coli K-antigen group 2 and group 3 typing database

This work aims to explore the differences between Python and Julia and to propose a detailed overview of the best-suited applications for each language. The repository includes mechanistic models in both Python and Julia.

An ensemble of plasmid classification tools

Presentations and work done for University of Pittsburgh course, Synthetic Biology.

This is a pipeline that can be used to generate a phylogenetic tree, including a heatmap showing carriage of specific genes, the assigned phylogroup of each strain, and the names of each strain. It should now be capable of working with any sort of strains - currently I'm working on making small improvements.

Bacterial motility patterns adapt smoothly in response to spatial confinement and disorder [Zhang H., Wetherington M.T., Ko H., FitzGerald C.E., Luzzatto L.V., Kovács I.A., Munro E.M., Nirody J.A.]

Collection of 1069 Escherichia coli virulence factors

Determines the serotype and virulence in Escherichia coli isolates using NGS data (reads) through kmer alignment.

The Monorepo for all things Toronto Beaches

Using machine learning to predict E. coli phenotypes

A command-line tool for predicting K-antigen type classifications in Escherichia coli.

Nanopore base caller based on original Chiron adding Dropout and SRU

In-silico synthetic biology design for low-odor, violet-glowing E. coli with experimental cellulose breakdown.

🧬 AI-powered multi-task model predicting E. coli resistance to Ciprofloxacin, Ceftriaxone & Amoxicillin from genomic features | AUC ~0.934 | Flask + RandomForest

Bash scripts to run virulencefinder and serotypefinder in local settings on ecoli fasta and fastq.gz files.

Machine learning - breast cancer and ecoli - classification

Ecoli related analysis for the SOFI platform.