St. JudePathogen-specific Shiny apps and reproducible pipelines for tracking amino acid variation, clade evolution, and lineage patterns across respiratory viruses and Nextclade3-supported pathogens.
Developed by Center for Applied Bioinformatics @ St. Jude Children's Research Hospital.
Public Shiny applications for scanning clade-aware amino acid changes across respiratory virus datasets and other Nextclade3-supported pathogens.
Dedicated apps for RSV, SARS-CoV-2, and human Influenza datasets.
Visualize amino acid variation across RSV clades and lineages.
Data source: Nextstrain
Track amino acid changes across SARS-CoV-2 clades.
Data source: Nextstrain
Explore amino acid variation in human influenza viruses.
Data source: GISAID
A flexible viewer for NextAA outputs from any supported Nextstrain dataset.
Universal Explorer for NextAA outputs from any Nextstrain dataset supported by Nextclade3. Current data: Chikungunya virus.
Data source: Nextstrain
The RVEAtlas Skill helps AI coding agents install and run COVIDExplorer, RSVExplorer, FLUExplorer, and AAExplorer locally. It can preview the setup with a dry run, download app code and release data, install missing R packages, and launch the selected Shiny app in a browser.
Use the RVEAtlas skill to install and run RSVExplorer locally. Install it into ~/RVEAtlasApps. Start with a dry run, then do the real install if the dry run looks correct.
Workflows for transforming global sequence resources into amino acid annotations and clade-aware explorer inputs.
Processes Nextstrain data for Nextclade3-supported pathogens into standardized amino acid variation outputs for AAExplorer and pathogen-specific explorers.
Processes GISAID human influenza data into amino acid variation summaries for the FLU Explorer.
From global sequence datasets to accessible visual summaries for pathogen evolution research.
RVE Atlas brings together public visualization apps and processing pipelines so researchers can move quickly from clade context to amino acid variation patterns across COVID, RSV, human influenza, and Nextstrain pathogens supported by Nextclade3.
