vivaldi

vivaldi (Viral Variant Location and Diversity) is an R package for analyzing viral genomes using next generation DNA sequencing.

The standard input is a vcf file.

Installation from CRAN

install.packages("vivaldi")

To get a bug fix or to use a feature from the development version, you can install the development version of vivaldi from GitHub.

# install.packages("devtools")
devtools::install_github("GreshamLab/vivaldi")

Authors: Marrisa Knoll, Katherine Johnson, Megan Hockman, Eric Borenstein, Mohammed Khalfan, Elodie Ghedin, David Gresham

If you use vivaldi in published research, please cite:

Roder, A. E., et al. "Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data." bioRxiv (2022): 2021-05 URL https://www.biorxiv.org/content/10.1101/2021.05.05.442873v2

Name		Name	Last commit message	Last commit date
Latest commit History 375 Commits
.github		.github
R		R
data		data
inst		inst
man		man
tests		tests
vignettes		vignettes
.Rbuildignore		.Rbuildignore
.gitignore		.gitignore
DESCRIPTION		DESCRIPTION
LICENSE		LICENSE
NAMESPACE		NAMESPACE
README.md		README.md
vivaldi.Rproj		vivaldi.Rproj