phage
There are 35 repositories under phage topic.
deprekate/PHANOTATE
PHANOTATE: a tool to annotate phage genomes.
Kalan-Lab/zol
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
bobeobibo/phigaro
Phigaro is a scalable command-line tool for predicting phages and prophages
clb21565/mobileOG-db
code repo for mobileOG-db
tseemann/phastaf
Identify phage regions in bacterial genomes for masking purposes
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
mshamash/OnePetri
Accelerate common Petri dish assays with AI.
Kalan-Lab/codoff
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.
deepomicslab/Graphage
This is the repository for GraphPhage, a phage analysis tool that integrates phage and ICE discrimination, phage integration site prediction, phage lifestyle prediction, and phage host prediction.
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
Dreycey/PhageScanner
A reconfigurable machine learning pipeline for labeling ORFs/proteins in bacteriophage genomes and metagenomic data.
linsalrob/PhageProteomicTree
The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance
jlmaier12/TrIdent
TrIdent- Transduction Identification: Automatic detection, classification and characterization of active transduction events in microbiomes.
naturepoker/Telephage
From protein to phage phylogeny in single line!
SchlossLab/Hannigan_ConjunctisViribus_ploscompbio_2018
Using graph database techniques to understand the infectious relationships between bacteria and phages.
xlxs4/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
andreaskuster/igem19-ethz-phage-hw-model
iGEM 19 Synthetic Biology
caleb-collar/motif-sniffer
Report, proposal, and mvp implementation of a simple tool for use in finding motifs in genome data. 🧬
CuiDachao/DeepVOG
A powerful deep learning (DL) tool and the trained models for the phage gene and protein identification with convolutional neural network (CNN).
FrancisGrace/iGEM-2020-DUT_China
2020 International Genetically Engineered Machine competition
naturepoker/phaster_kits
Quality of life improvement scripts for working with https://phaster.ca (PHAge Search Tool Enhanced Release)
Strong-Lab/Viral_Classification_in_Metagenomics
This repository contains the data and scripts used in Simulation Study of Viral Contiguous Sequence Identification Tools
xlxs4/bacteria-phage-abm.jl
A toy Agent-Based Model of the coevolution dynamics between bacteria and phages, with a focus on environment structure
YitongTseo/ml_phage_display
Code for Next Generation Phage Display Motif Denoising and Identification
AMbioinformatics/Host4Phage
Prediction of bacterial host for phage
JoshuaIszatt/phanta
Illumina short read assembly data pipeline for phage
JoshuaIszatt/phunky
Nanopore long read assembly data pipeline for phage genomes
m414rkie/Phage-to-Shark
Phage to Shark
rebear217/PhageMFiles
.m, .MAT, .PDF, .XLS files for "Canonical host-pathogen tradeoffs subverted by mutations with dual benefits"
UPOBioinfo/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.
janzheng/open-phage
A micro-site for teaching and learning microbiology and bacteriophage wet lab skills
matthewcso/Temperate-Phage-Modelling-3BM6
Old repository comprising code for my HTHSCI 3BM6 phage modelling project.
xlxs4/bacteria-phage-abm
An Agent-Based Model simulating the coevolution dynamics between phages and bacteria. Was my essay in the ABM course by SFI