Scripts to support preparation and analysis of SARS CoV 2 phylogenetic analyses.
Archived version of sarscov2Rutils package as used for the production of skyline plots and importation dates for the paper 'Saudi Arabian SARS-CoV-2 genomes implicate a mutant Nucleoplasmid protein in modulating host interactions and increased viral load in COVID-19 patients'
Version: 0.1.4
Date: 2020-06-17
Code Contributors: Erik M Volz, Manon Ragonnet, David Jorgensen, Lily Geidelberg, Olivia Boyd, Robert Johnson, Igor Siveroni
Maintainer: Erik M Volz erik.volz@gmail.com
License: LGPL
Required R packages: ape, treedater(>=0.5.0), lubridate, ggtree, ggplot2, treeio, knitr, coda, phangorn, Hmisc, yaml, glue
Suggested R packages: pika, dplyr, skygrowth, seqinr, treestructure, Biostrings
Tested R version: 3.6.3
Tested OS: Windows 10.0, MacOS 10.14, Linux CentOS 7
Tested dependencies: ape 5.4, treedater 0.5.0, lubridate 1.7.9, ggtree 1.16.6, ggplot2 3.3.2, treeio 1.8.2, knitr 1.29, coda 0.19-3, phangorn 2.5.5, Hmisc 4.4-0, yaml 2.2.1, glue 1.4.1
Certain functions in this R package also require IQ-TREE (version 1.6.12-Windows tested) and MAFFT (version 7.450-win64 tested) and interact with these programs via system calls from R. Adding these programs to PATH is reccomended, or modifications can be made to these functions.
Download tar file and install from package archive file.
install.packages(path_to_tar_file, repos = NULL, type="source")
Typical install time < 1 minute (not incluing R installation and package dependencies).