# From CRAN - Official release:
install.packages("SCpubr")
# From GitHub - Latest stable development version:
if(!requireNamespace("devtools", quietly = TRUE)){
install.packages("devtools") # If not installed.
}
devtools::install_github("enblacar/SCpubr", ref = "v1.1.1-dev-stable")
Installation guide
This package can be installed using the following commands:
Further packages are needed in order to run the different functions:
# Install CRAN packages.
cran_packages <- c("assertthat",
"circlize",
"colorspace",
"dplyr",
"ggbeeswarm",
"ggdist",
"ggExtra",
"ggnewscale",
"ggplot2",
"ggplotify",
"ggrastr",
"ggrepel",
"ggridges",
"ggsignif",
"graphics",
"magrittr",
"patchwork",
"pheatmap",
"plyr",
"rlang",
"scales",
"scattermore",
"Seurat",
"tibble",
"tidyr",
"forcats",
"Matrix",
"purrr",
"stringr",
"svglite",
"viridis")
install.packages(cran_packages)
# Install bioconductor packages.
bioconductor_packages <- c("AUCell",
"ComplexHeatmap",
"clusterProfiler",
"enrichplot",
"infercnv",
"Nebulosa",
"UCell")
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(bioconductor_packages)
# Install github packages.
github_packages <- c("ggsankey",
"liana",
"monocle3")
if (!requireNamespace("remotes", quietly = TRUE))
install.packages("remotes")
remotes::install_github(github_packages)
One can check the dependencies by running SCpubr::state_dependencies()
.