hiv
There are 79 repositories under hiv topic.
cbg-ethz/V-pipe
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
EMOD-Hub/EMOD
Source files for building the IDM EMOD disease transmission model.
CDCgov/MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
niemasd/FAVITES
FAVITES (FrAmework for VIral Transmission and Evolution Simulation)
EpiModel/EpiModelHIV
Network Models of HIV Transmission Dynamics among MSM and Heterosexuals
AMPATH/ng2-amrs
Point of care system for AMPATH clinics
AABoyles/MicrobeTrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
hivdb/codfreq
FASTQ-to-CodFreq pipeline for HIV-1 and SARS-CoV-2
theLongLab/CATE
A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data.
HKU-BAL/ClusterV
ClusterV: finding HIV quasispecies and drug resistance from ONT sequencing data
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
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 small molecules, including a lack of validated quantitative structure-activity relationships (QSAR). Herein, we developed QSAR models that quantitatively predict both thermodynamic and kinetic-based binding parameters of small molecules and the HIV-1 TAR model system. Small molecules bearing diverse scaffolds was screened against the HIV-1 TAR using surface plasmon resonance. Then multiple linear regression (MLR) combined with feature selection was performed to afford robust models that allowed direct interpretation of properties critical for both binding strength and kinetic rate constants. These models were externally validated with new molecules and their accurate performance confirmed via comparison to ensemble tree methods.
SACEMA/inctools
Incidence Estimation Tools
MullinsLab/viroverse
a platform for the collection, storage, retrieval, and analysis of experimental data for laboratory workflows
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
ahmedaq/RocaSec
RocaSec: A standalone GUI-based package for robust co-evolutionary analysis of proteins
deforay/vlsm
A simple, open source Sample Management System for Viral Load, EID and Covid-19 testing.
deforay/vlsm-interfacing
Viral Load Sample Management - Machine Interfacing
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"
EvoNetHIV/EvoNetHIV
Current development version of EvoNetHIV package
fcrawford/indiana-hiv
Reconstruction and analysis of the HIV outbreak in Scott County, Indiana
gallardo-seq/MrHAMER
High accuracy single molecule Nanopore reads using the MrHAMER pipeline
iliapopov17/The-shadow-of-HIV
🦠Research project in Bioinformatics Institute 2023-2024
InstituteforDiseaseModeling/docs-emod-scenarios
Tutorial materials as referenced in IDM's documentation for EMOD, an agent-based disease dynamics model.
MullinsLab/ISDB
A toolkit for creating databases of viral integration sites in host genomes
ahmedaq/RoCA
Software for identifying co-evolutionary sectors in proteins using RoCA
cfe-lab/CFEIntact
A bioinformatics tool for detecting defects in HIV-1 proviral sequences.
iiithf/virology
Virology is the study of viruses – submicroscopic, parasitic particles of genetic material contained in a protein coat – and virus-like agents.
SineadMorris/ushr
Understanding suppression of HIV in R
STTLab/HIV-64148
HIV-64148, an integration of multiple long-read genome assemblers with a pipeline for analysis of HIV-1 genomic data from Oxford Nanopore Sequencing Technology or PacBio Real-Time (SMRT) Sequencing technology.
AlfredUg/HIVseqDB
Webserver for storage [and analysis] of NGS-based HIVDR testing data
FrederickHuangLin/Gut-Microbiome-and-Sexual-Behavior
Scripts and outputs for the paper "High risk sexual behavior is linked to changes in gut microbiome and systemic inflammation that lead to HIV-1 infection in men who have sex with men"
sevenfalling/tag
This repository will used to gather and distribute intelligence about the The AIDS-cure Genocide started by Gilead Sciences which includes the CIA's massacres of houses of worship.
Snigdha1008/TB_Burden_Analysis
I created various dashboards to ascertain (a)Prevalence of all forms of TB across various countries divided into 6 regions, (b)Distribution of mortality, (c) Evaluation of Mortality (d)Comorbidities with HIV
vembha/SIV_natural_control
Code repository for the publication. Contains Monolix and Julia files used for parameter estimation and data analysis, respectively.