V-pipe is a pipeline designed for analysing NGS data of short viral genomes
Source files for building the IDM EMOD disease transmission model.
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
FAVITES (FrAmework for VIral Transmission and Evolution Simulation)
Network Models of HIV Transmission Dynamics among MSM and Heterosexuals
A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests and viral simulations at scale. Related manuscripts: https://doi.org/10.1111/2041-210X.14168 and https://doi.org/10.1038/s41467-025-60988-8
Point of care system for AMPATH clinics
FASTQ-to-CodFreq pipeline for HIV-1 and SARS-CoV-2
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
ClusterV: finding HIV quasispecies and drug resistance from ONT sequencing data
Clinical Trial Risk Tool for analysing clinical trial protocols using natural language processing and assessing the risk of ending uninformatively, developed by Fast Data Science
The diversity of RNA structural elements and their documented role in human diseases make RNA an attractive therapeutic target. However, progress in drug discovery and development has been hindered by challenges in the determination of high-resolution RNA structures and a limited understanding of the parameters that drive RNA recognition by smal…
Incidence Estimation Tools
a platform for the collection, storage, retrieval, and analysis of experimental data for laboratory workflows
A repository for the Advanced Programming Tutorial that teaches you how to develop an interactive model using Shiny
This repo contains the data and software used to run the analyses in the "Using machine learning and Big data to explore the drug resistance landscape in HIV"
A comprehensive pipeline for HIV drug resistance identification, variant evaluation, and surveillance.
Viral Load Sample Management - Machine Interfacing
RocaSec: A standalone GUI-based package for robust co-evolutionary analysis of proteins
🦠Research project in Bioinformatics Institute 2023-2024
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