Tomas J. Aragon [aut], Michael P. Fay
[ctb], Daniel Wollschlaeger [ctb], Adam Omidpanah [cre, ctb]

c(person("Tomas J. Aragon", "Developer", role = c("aut",
"cre"), email = "aragon@berkeley.edu"), person("Michael P.
Fay", "User", role = "ctb", email = "mfay@niaid.nih.gov"),
person("Daniel Wollschlaeger", "User", role = "ctb", email =
"dwoll@psychologie.uni-kiel.de"))
Tomas J. Aragon Developer [aut, cre], Michael P. Fay User
[ctb], Daniel Wollschlaeger User [ctb]
Tomas J. Aragon Developer <aragon@berkeley.edu>

A suite of tools to predict peptide MHC (major histocompatibility complex) presentation in the context of both human and mouse. Polymorphic peptides between self and foreign proteins are identified. The ability of peptides to bind self MHC is assessed and scored. Based on half maximal inhibitory concentration as queried through the immune epitope database API <http://tools.iedb.org/mhcii/> using user defined methods, the foreign peptides most likely to be presented are output along with their predicted binding strength, amino acid position, the protein from which each peptide was derived, and the presenting allele. "References:" Vita R, Mahajan S, Overton JA, Dhanda SK, Martini S, Cantrell JR, Wheeler DK, Sette A, Peters B. <doi:10.1093/nar/gky1006>.
c(person("Joan","Zhang",email = "joan.zhang@emory.edu", role = c("aut", "cre")),
person("Aileen","Johnson",email = "aileen.johnson@emory.edu ", role = c("aut")),
person("Christian P","Larsen",email = "clarsen@emory.edu", role = c("cph", "aut")))
devtools, dplyr, usethis, rstudioapi, fs, here, httr, janitor,
purrr, stringr, tibble, tidyverse, utils, readr, ggseqlogo,
Biostrings, msa, seqinr
Joan Zhang [aut, cre],
Aileen Johnson [aut],
Christian P Larsen [cph, aut]

devtools, dplyr, usethis, rstudioapi, fs, here, httr, janitor,
purrr, stringr, tibble, tidyverse, utils, readr, ggseqlogo,
Biostrings, seqinr

dplyr, fs, here, httr, janitor, purrr, stringr, tibble,
tidyverse, utils, readr, Biostrings, seqinr

Small Helpers and Tricks for Epidemics Analysis
c(person("Thibaut", "Jombart", email = "thibautjombart@gmail.com", role = c("aut", "cre")),
person("Anne", "Cori", email = "a.cori@imperial.ac.uk", role = c("aut")))
A collection of small functions useful for epidemics analysis and infectious disease modelling. This includes computation of basic reproduction numbers from growth rates, generation of hashed labels to anonymise data, and fitting discretised Gamma distributions.
testthat, roxygen2, outbreaks, incidence, knitr, rmarkdown
Thibaut Jombart [aut, cre],
Anne Cori [aut]