Covmuller

Covmuller is an R-package designed for analysis of sequencing metadata deposited on GISAID.

Features

Covmuller currently supports the following features:

• Read and preprocess metadata file downloaded from GISAID: Vignette
• Plot variant prevalence: Vignette
• Fit multinomial models to variant prevalence data:
  • India
  • USA
  • Canada
  • UK
  • Australia
  • SouthAfrica
• Estimate totals prevalence of variants by projecting case prevalence data on multinomial fits:
  • Countries/States:
    • India
    • New York state
    • South Africa
    • United Kingdom
    • USA
  • Cities:
    • New York City (USA)
    • Delhi (India)
    • Mumbai (India)
    • Maharashtra (India)
    • Pune (India)