Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
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Updated
Sep 16, 2024 - Rust
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
The Flexible Epidemic Modeling Pipeline
🛡Crowd-sourced COVID-19 reporting and assessment system.
Import script needed to build FluPRINT database from source 💻
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
MPH Capstone Data Management & Analysis
Influenza-like illness prediction model
Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution
Linked Multilocus Genotype by Sequencing (LMGSeq) applied to high-throughput quantification of genetic exchange among diverse human Influenza A virus strains
A Python script that sends Italian flu updates to Mastodon
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