Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

An experimental deep learning & genotype network-based system for predicting new influenza protein sequences.

Influenza forecasts visualizer

🛡Crowd-sourced COVID-19 reporting and assessment system.

The Moving Epidemic Method Shiny Web Application

The Moving Epidemic Method R Package

Import script needed to build FluPRINT database from source 💻

Flu clade and mutation frequencies

The Flexible Epidemic Modeling Pipeline

We apply combinatorial mutagenesis and next-generation sequencing to characterize the local fitness landscape in an antigenic region of NA in six different human H3N2 strains that were isolated around 10 years apart. This pipeline is used to analyze data and plotting.

Shiny app for FSN model comparison

RECDS identifies cluster-transition determining sites underlying the antigenic evolution of seasonal influenza viruses

Query the 'CMU' 'DELPHI' Epidemiological Data 'API' (package wrapper https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.R)

vSNP -- validate SNPs

stochastic modeling | HMM

Nanopore based RNA-Seq pipeline for viral samples

Im Datensatz "Laborbestätigte Influenzafälle in Deutschland" werden die wöchentlichen Fallzahlen und Inzidenzen (Fälle pro 100.000 Personen) der nach den Vorgaben des Infektionsschutzgesetzes (IfSG) von den Gesundheitsämtern in Deutschland an die zuständigen Landesbehördne und das Robert Koch-Institut (RKI) übermittelten laborbestätigt...

Influenza-like illness prediction model

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

KDHE Influenza A pipeline, built to take MinIon fastq files and produce clade analysis