I have some problem to reproduce this excellent work.
seems that voom is a package that is hard to find
Reader from Hoekstra, M. E., Slagter, M., Urbanus, J., Toebes, M., Slingerland, N., de Rink, I., Kluin, R. J. C., Nieuwland, M., Kerkhoven, R., Wessels, L. F. A., & Schumacher, T. N. (2024). Distinct spatiotemporal dynamics of CD8+ T cell-derived cytokines in the tumor microenvironment. Cancer Cell, 42(1), 157-167.e159. https://doi.org/10.1016/j.ccell.2023.12.010
cit_pkgs <- c('devtools', 'ComplexHeatmap', 'credentials', 'milo', 'sctransform', 'voom', 'glmnet')
pkgs <- c('miloR', 'car',
'parsnip', 'tidymodels', 'yardstick', 'ranger', 'kknn',
'devtools', 'curl', 'targets', 'ggpubr', 'ArrayExpress',
'umap', 'progressr', 'rsample',
'Hmisc',
'glmnet',
'preprocessCore', 'envnames', 'voom',
'pracma', 'targets',
'DESeq2', 'wesanderson',
'biomaRt', 'furrr', 'fgsea', 'naturalsort',
'tidyverse', 'knitr',
'tikzDevice',
'scran', 'SingleCellExperiment', 'limma', 'edgeR', 'ROCR',
'devtools', 'Seurat', 'GGally', 'knitr', 'pacman', 'circlize',
'NMF', 'e1071')
already_cited <- c('targets', 'glmnet', 'milo', 'sctransform', 'voom')
for (p in pkgs) {
try_install(p)
}
U_lib_dir <- if (dir.exists('/libs')) '/libs' else '/u_libs'
if (F && !require('credentials', character.only = T, quietly = T)) {
remotes::install_github("r-lib/credentials", lib = R_lib_dir)
}
if (!require('ComplexHeatmap', character.only = T, quietly = T)) {
install_github('Jokergoo/ComplexHeatmap')
library(ComplexHeatmap)
}
if (!require('maartenutils', character.only = T, quietly = T)) {
install_github('slagtermaarten/maartenutils')
}
if (!require('genesets', character.only = T, quietly = T)) {
install_github('slagtermaarten/genesets')
}