Prediction of bacterial host for phage
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Updated
Jun 2, 2022 - C++
Prediction of bacterial host for phage
Old repository comprising code for my HTHSCI 3BM6 phage modelling project.
PhageOrder is a python package designed to reorder phage genomes based on its terminase subunit.
Configurable short read de novo assembly container using SPAdes and bbmap
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.
An Agent-Based Model simulating the coevolution dynamics between phages and bacteria. Was my essay in the ABM course by SFI
.m, .MAT, .PDF, .XLS files for "Canonical host-pathogen tradeoffs subverted by mutations with dual benefits"
Quick and dirty scripts for simple biology
A powerful deep learning (DL) tool and the trained models for the phage gene and protein identification with convolutional neural network (CNN).
A toy Agent-Based Model of the coevolution dynamics between bacteria and phages, with a focus on environment structure
Quality of life improvement scripts for working with https://phaster.ca (PHAge Search Tool Enhanced Release)
Report, proposal, and mvp implementation of a simple tool for use in finding motifs in genome data. 🧬
This repository contains the data and scripts used in Simulation Study of Viral Contiguous Sequence Identification Tools
2020 International Genetically Engineered Machine competition
Active prophage detection in metagenome sequencing read coverages
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