174 skills found · Page 1 of 6
mrc-ide / Covid SimThis is the COVID-19 CovidSim microsimulation model developed by the MRC Centre for Global Infectious Disease Analysis hosted at Imperial College, London.
sanger-pathogens / RoaryRapid large-scale prokaryote pan genome analysis
SORMAS-Foundation / SORMAS ProjectSORMAS (Surveillance, Outbreak Response Management and Analysis System) is an early warning and management system to fight the spread of infectious diseases.
ersilia-os / ErsiliaThe Ersilia Model Hub, a repository of AI/ML models for infectious and neglected disease research.
sanger-pathogens / Snp SitesFinds SNP sites from a multi-FASTA alignment file
EpiModel / EpiModelMathematical Modeling of Infectious Disease Dynamics
sanger-pathogens / ArtemisArtemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
sanger-pathogens / CirclatorA tool to circularize genome assemblies
nickjcroucher / GubbinsRapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
CSSEGISandData / COVID 19 Unified DatasetUnified COVID-19 Dataset
sanger-pathogens / AribaAntimicrobial Resistance Identification By Assembly
sanger-pathogens / Assembly StatsGet assembly statistics from FASTA and FASTQ files
cidgoh / DataHarmonizerA standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.
OpenGene / FastvAn ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.
chanzuckerberg / Czid WebInfectious Disease Sequencing Platform
sanger-pathogens / Pathogen Informatics TrainingNo description available
jangevaare / Pathogen.jlSimulation, visualization, and inference of individual level infectious disease models with Julia
sanger-pathogens / FastaqPython3 scripts to manipulate FASTA and FASTQ files
adamkucharski / 2020 NcovAccompanying code for: Kucharski AJ, Russell TW et al. Early dynamics of transmission and control of COVID-19: a mathematical modelling study. Lancet Infectious Diseases, 2020
epinowcast / EpinowcastA modular Bayesian framework for real-time infectious disease surveillance. Provides tools for nowcasting, reproduction number estimation, delay estimation, and forecasting from data subject to reporting delays, right-truncation, missing data, and incomplete ascertainment
