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V-pipe

cbg-ethz /V-pipe

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

bioinformatics snakemake virus genomics ngs sequencing conda bioinformatics-pipeline hiv sars-cov-2 sarscov2 biohackeu20 biohackcovid20 biohackeu21 biohackeu22

UpdatedMar 13, 2025
Jupyter Notebook

EMOD-Hub /EMOD

Source files for building the IDM EMOD disease transmission model.

modeling idm stochastic epidemiology malaria hiv

UpdatedJan 15, 2025
C

MicrobeTrace

CDCgov /MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

bioinformatics genomics phylogenetic-trees phylogenetics epidemiology network-visualization hiv cdc phylogenomics phylogeny sequence-alignment genomic-data-analysis genomics-visualization pathogens

UpdatedFeb 6, 2025
TypeScript

niemasd /FAVITES

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

docker modular virus simulation evolution transmission phylogenetics robust hiv evolution-simulator transmission-network

UpdatedNov 11, 2023
Python

EpiModel /EpiModelHIV

Network Models of HIV Transmission Dynamics among MSM and Heterosexuals

network-graph agent-based-modeling epidemiology hiv mathematical-modelling hiv-transmission-dynamics statnet

UpdatedSep 12, 2022
R

AMPATH /ng2-amrs

Point of care system for AMPATH clinics

emr diabetes ehr hiv referrals amrs point-of-care oncology openmrs-point-of-care chronic-diseases

UpdatedJan 7, 2025
TypeScript

CATE

theLongLab /CATE

A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data.

genome genetics anaconda cuda conda vcf epidemiology hiv viral-genomics 1000genomes evolutionary-biology neutrality ehh mk-test epidemic-simulations sars-cov-2 extended-haplotype-homozygosity tajima

UpdatedMar 16, 2025
Cuda

AABoyles /MicrobeTrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

bioinformatics genomics network-graph phylogenetic-trees phylogenetics epidemiology network-visualization network-analysis hiv cdc phylogenomics phylogeny sequence-alignment genomic-data-analysis genomics-visualization pathogens

UpdatedSep 13, 2024
HTML

hivdb /codfreq

FASTQ-to-CodFreq pipeline for HIV-1 and SARS-CoV-2

hiv ngs-pipeline sars-cov-2

UpdatedMar 21, 2024
Python

HKU-BAL /ClusterV

ClusterV: finding HIV quasispecies and drug resistance from ONT sequencing data

bioinformatics nanopore hiv nanopore-sequencing hivdb subtype-finding

UpdatedJan 7, 2025
Python

hargrove-lab /QSAR

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…

machine-learning rna hiv qsar lasso-regression

UpdatedMar 21, 2023
R

clinical_trial_risk

fastdatascience /clinical_trial_risk

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

nlp machine-learning natural-language-processing natural-language clinical-trials hiv nlp-machine-learning pharma tuberculosis natural-language-understanding tb pharmaceuticals

UpdatedJan 29, 2025
Jupyter Notebook

SACEMA /inctools

Incidence Estimation Tools

cran statistics biostatistics epidemiology hiv incidence biomarkers infectious-diseases incidence-estimation incidence-inference

UpdatedAug 10, 2022
R

R-HTA-in-LMICs /Advanced-Tutorial-2022

A repository for the Advanced Programming Tutorial that teaches you how to develop an interactive model using Shiny

tutorial r shiny advanced hta hiv cost-effectiveness health-economics interactive-models

UpdatedJan 23, 2023
R

MicroBioGenoHub /HIV-DRIVES

A comprehensive pipeline for HIV drug resistance identification, variant evaluation, and surveillance.

bioinformatics pipeline surveillance sequencing bioinformatics-pipeline hiv drug-resistance bioinformatics-tool lentivirus humimdef1

UpdatedJul 18, 2024
Shell

MullinsLab /viroverse

a platform for the collection, storage, retrieval, and analysis of experimental data for laboratory workflows

laboratory webapp microbiology hiv

UpdatedDec 9, 2022
Perl

lucblassel /HIV-DRM-machine-learning

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"

machine-learning paper hiv

UpdatedJan 20, 2022
Jupyter Notebook

ahmedaq /RocaSec

RocaSec: A standalone GUI-based package for robust co-evolutionary analysis of proteins

gui virus analysis tool standalone protein software robust hiv hepatitis roca hcv sectors co-evolving residues hepatitis-c biochemical-domains evolutionary-analysis standalone-gui inferred-sectors

UpdatedDec 18, 2019

iliapopov17 /The-shadow-of-HIV

🦠Research project in Bioinformatics Institute 2023-2024

snakemake dna beta-diversity iontorrent hiv samtools bowtie2 relative-abundances alpha-diversity kraken2 differential-abundance-analysis maaslin2

UpdatedAug 16, 2024
Jupyter Notebook

deforay /vlsm

A simple, open source Sample Management System for Viral Load, EID and Covid-19 testing.

lis hiv eid viral-load covid-19 covid19

UpdatedMar 14, 2025
PHP

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