A method to estimate population coverage for a set of epitopes adjusted for immunoprevalence
Developed by Torfinn Støve Madssen and Even Holth Rustad
Accompanying the manuscript: Prevalent and immunodominant CD8 T-cell epitopes are conserved in SARS-CoV-2 variants (Meyer, Blaas, Bollineni, et al.)
The enclosed Rmd and data files are sufficient to reproduce the analysis and figures shown in the paper. All analyses should run in < 5 minutes on a standard computer, provided the required R packages are installed.
Developed and tested on the following system:
R version 4.0.4 (2021-02-15) macOS Big Sur 10.16
Package versions:
gdata_2.18.0
stringi_1.6.1
RColorBrewer_1.1-2
openxlsx_4.2.3
reshape2_1.4.4
forcats_0.5.1
stringr_1.4.0
dplyr_1.0.6
purrr_0.3.4
readr_1.4.0
tidyr_1.1.3
tibble_3.1.2
ggplot2_3.3.5
tidyverse_1.3.0
