https://github.com/saketkc/covmuller

Covmuller is an R-package designed for analysis of SARS-CoV-2 sequencing metadata deposited on GISAID
https://github.com/saketkc/covmuller

Last synced: 24 days ago
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Covmuller is an R-package designed for analysis of SARS-CoV-2 sequencing metadata deposited on GISAID

• Host: GitHub
• URL: https://github.com/saketkc/covmuller
• Owner: saketkc
• License: mit
• Created: 2022-03-03T00:48:35.000Z (over 2 years ago)
• Default Branch: master
• Last Pushed: 2024-04-17T03:10:27.000Z (7 months ago)
• Last Synced: 2024-04-17T08:17:57.467Z (7 months ago)
• Language: R
• Homepage: http://saket-choudhary.me/covmuller/
• Size: 7.94 GB
• Stars: 3
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: CITATION.cff

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README

        
# Covmuller

Covmuller is an R-package designed for analysis of SARS-CoV-2 sequencing metadata deposited on [GISAID](https://www.gisaid.org/). 

![](https://saket-choudhary.me/covmuller/articles/SouthAfrica_contrast_India_files/figure-html/unnamed-chunk-3-1.png)

![](https://raw.githubusercontent.com/saketkc/covmuller/master/docs/articles/SA_animated.gif)

## Features

Covmuller currently supports the following features:

* Read and preprocess metadata file downloaded from GISAID: [Vignette](articles/Introduction.html)

* Plot variant prevalence: [Vignette](articles/Introduction.html)

* Fit multinomial models to variant prevalence data:

    - [India](https://saket-choudhary.me/covmuller/articles/MultinomialModeling_India.html)

    - [USA](https://saket-choudhary.me/covmuller/articles/MultinomialModeling_USA.html)

    - [Canada](https://saket-choudhary.me/covmuller/articles/MultinomialModeling_Canada.html)

    - [UK](https://saket-choudhary.me/covmuller/articles/MultinomialModeling_UK.html)

    - [Australia](https://saket-choudhary.me/covmuller/articles/MultinomialModeling_Australia.html)

    - [SouthAfrica](https://saket-choudhary.me/covmuller/articles/MultinomialModeling_SouthAfrica.html)

* Estimate totals prevalence of variants by projecting case prevalence data on multinomila fits:  

    - [India](https://saket-choudhary.me/covmuller/articles/VariantAnimation-India.html)

    - [New York state](https://saket-choudhary.me/covmuller/articles/VariantAnimation-NewYork.html)

    - [New York City](https://saket-choudhary.me/covmuller/articles/VariantAnimation-NYC.html)

    - [South Africa](https://saket-choudhary.me/covmuller/articles/VariantAnimation-SouthAfrica.html)

    - [United Kingdom](https://saket-choudhary.me/covmuller/articles/VariantAnimation-UK.html)

    - [USA](https://saket-choudhary.me/covmuller/articles/VariantAnimation-USA.html)