codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the full genome.
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Updated
May 24, 2024 - Python
codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the full genome.
TrIdent- Transduction Identification: Automatic detection, classification and characterization of active transduction events in microbiomes.
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
Configurable short read de novo assembly container using SPAdes and bbmap
Quality of life improvement scripts for working with https://phaster.ca (PHAge Search Tool Enhanced Release)
PHANOTATE: a tool to annotate phage genomes.
PhageOrder is a python package designed to reorder phage genomes based on its terminase subunit.
Active prophage detection in metagenome sequencing read coverages
DEPRECATED: Discover divergent virus sequences, prune flanking cellular sequences, make basic report
Phigaro is a scalable command-line tool for predicting phages and prophages
An Agent-Based Model simulating the coevolution dynamics between phages and bacteria. Was my essay in the ABM course by SFI
code repo for mobileOG-db
A reconfigurable machine learning pipeline for labeling ORFs/proteins in bacteriophage genomes and metagenomic data.
Repository containing trained YOLOv5 object detection models used within OnePetri for Petri dish and plaque detection.
Accelerate common Petri dish assays with AI.
Scripts to analyze the data for the paper "An outstanding bacterial membranome requires CRISPR-Cas systems to avoid the intervention of phages" and derive the figures or subfigures shown in the manuscript.
.m, .MAT, .PDF, .XLS files for "Canonical host-pathogen tradeoffs subverted by mutations with dual benefits"
A toy Agent-Based Model of the coevolution dynamics between bacteria and phages, with a focus on environment structure
A toy MC model studying bacteria-phage coevolution dynamics. Code is meant to be readable instead of performant, or, well, good. Good for beginners in ABM
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