phage
There are 0 repository under phage topic.
- Language:Python 65
- Language:HTML 46
Kalan-Lab / zol
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
Language:Python 36- Language:Perl 29
- mobileOG-db
clb21565 / mobileOG-db
code repo for mobileOG-db
Language:Python 24 linsalrob / PhageHosts
This is the complete code base used in Robert A. Edwards, Katelyn McNair, Karoline Faust, Jeroen Raes, and Bas E. Dutilh (2015) Computational approaches to predict bacteriophage–host relationships. FEMS Microbiology Reviews doi: 10.1093/femsre/fuv048
Language:Python 15- Language:Swift 13
mshamash / OnePetri-models
Repository containing trained YOLOv5 object detection models used within OnePetri for Petri dish and plaque detection.
mtisza1 / Cenote_Unlimited_Breadsticks
DEPRECATED: Discover divergent virus sequences, prune flanking cellular sequences, make basic report
Language:Shell 6codoff: 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.
Language:Python 4The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance
Language:Perl 4Dreycey / PhageScanner
A reconfigurable machine learning pipeline for labeling ORFs/proteins in bacteriophage genomes and metagenomic data.
Language:Jupyter Notebook 3naturepoker / Telephage
From protein to phage phylogeny in single line!
Language:Shell 2SchlossLab / Hannigan_ConjunctisViribus_ploscompbio_2018
Using graph database techniques to understand the infectious relationships between bacteria and phages.
Language:PostScript 2xlxs4 / bacteria-phage-montecarlo
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
Language:Python 2- Language:Python 1
caleb-collar / motif-sniffer
Report, proposal, and mvp implementation of a simple tool for use in finding motifs in genome data. 🧬
Language:Python 1CuiDachao / DeepVOG
A powerful deep learning (DL) tool and the trained models for the phage gene and protein identification with convolutional neural network (CNN).
Language:Python 1FrancisGrace / iGEM-2020-DUT_China
2020 International Genetically Engineered Machine competition
Language:HTML 1jlmaier12 / TrIdent
TrIdent- Transduction Identification: Automatic detection, classification and characterization of active transduction events in microbiomes.
Language:HTML 1Quality of life improvement scripts for working with https://phaster.ca (PHAge Search Tool Enhanced Release)
Language:Shell 1Strong-Lab / Viral_Classification_in_Metagenomics
This repository contains the data and scripts used in Simulation Study of Viral Contiguous Sequence Identification Tools
Language:Jupyter Notebook 1A toy Agent-Based Model of the coevolution dynamics between bacteria and phages, with a focus on environment structure
Language:Julia 1YitongTseo / ml_phage_display
Code for Next Generation Phage Display Motif Denoising and Identification
Language:Jupyter Notebook 1AMbioinformatics / Host4Phage
Prediction of bacterial host for phage
Language:C++ 0- Language:Fortran 0
rebear217 / PhageMFiles
.m, .MAT, .PDF, .XLS files for "Canonical host-pathogen tradeoffs subverted by mutations with dual benefits"
Language:MATLAB 0UPOBioinfo / crispromeskape
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.
Language:Python 0- Language:Python 0
Binomica-Labs / easy-scripts
Quick and dirty scripts for simple biology
Language:Shelljanzheng / open-phage
A micro-site for teaching and learning microbiology and bacteriophage wet lab skills
Language:CSSJoshuaIszatt / PhageOrder
PhageOrder is a python package designed to reorder phage genomes based on its terminase subunit.
Language:PythonConfigurable short read de novo assembly container using SPAdes and bbmap
Language:Pythonmatthewcso / Temperate-Phage-Modelling-3BM6
Old repository comprising code for my HTHSCI 3BM6 phage modelling project.
Language:Jupyter NotebookAn Agent-Based Model simulating the coevolution dynamics between phages and bacteria. Was my essay in the ABM course by SFI
Language:NetLogo
