This package is still under active development. If you see this message, assume that several parts of the package don’t quite work yet.
agdist allows easy computation of antigenic distances.
These few lines of code produce a list of antigenic distances.
# install if needed - package is not yet on CRAN
# remotes::install_github('ahgroup/agdist')
library(agdist)
# load (and check) data
sequencedata <- read.csv("sequence-file.csv")
# compute distances
agdistances <- compute_distances(
sequencedata$aligned_sequences,
method = "p-epitope"
)
# look at results
agdistancesIf you think something like this is of interest to you, hop on over to the Quick Start tutorial (vignette).
To dig deeper, check out all available vignettes/tutorials for agdist.
The package website (if you are not already on it) is https://ahgroup.github.io/agdist/. You can access all the tutorials from there, as well as some additional information.
This R package was developed by Zane Billings and Andreas Handel. A full list of contributors and a Bibtex entry for the citation can be found here.
This project was/is partially supported by NIH grants XXX.