Common Covid Tasks

CCT combines a number of commonly requested covid related tasks into an easy(ish) to use package.

• Create a node network hierarchy from the pangolin lineages and aliases
• Cache that data locally in case of remote data or access problems
• Query that network for ancestors and descendants of a lineage
• Parse constellations into a easily used table
• Parse the covariants.org variant table
• Expand all the variants in that table into their children
• Sort lineages by ancestry instead of alnum

Installation Instructions

Clone Git Repository and Install Locally

install.packages("cct", repos = NULL, type="source")

or

remotes::install_local("cct")

Install from Github

remotes::install_github("TheZetner/cct")