SCENIC包安装

原创已于 2025-08-10 12:38:45 修改 · 1.2k 阅读

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于 2025-08-10 12:37:25 首次发布

该文章已生成可运行项目，

1.首先安装依赖包

if (!require("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}

install.packages("devtools")
library(devtools)

BiocManager::install(c("GENIE3", "AUCell", "RcisTarget"))
# Also required:
install.packages('zoo')
# Recommended to run AUCell:
BiocManager::install(c("mixtools", "rbokeh"))
# To visualize the binary matrices and perform t-SNEs:
BiocManager::install(c("NMF", "pheatmap", "Rtsne", "R2HTML"))
# To support paralell execution (not available in Windows):
BiocManager::install(c("doMC", "doRNG"))
# To export/visualize in http://scope.aertslab.orgif (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
devtools::install_github("aertslab/SCopeLoomR", build_vignettes = TRUE)
# Other dependencies for the examples (lower priority)
BiocManager::install(c("SingleCellExperiment"))
install.packages("dynamicTreeCut")

部分依赖包安装失败，可以下载包之后安装

devtools::install_local("C:\\Users\\admin\\Downloads\\rbokeh_0.5.2.tar.gz")
BiocManager::install(c("GENIE3", "RcisTarget"))
devtools::install_local("C:\\Users\\admin\\Downloads\\R2HTML_2.3.4.tar.gz")
devtools::install_local("C:\\Users\\admin\\Downloads\\doRNG_1.8.6.2.tar.gz")
install.packages("doMC", repos="http://R-Forge.R-project.org")

2.安装SCENIC
devtools::install_github("aertslab/SCENIC")

如果SCENIC没有安装成功，考虑下载后本地安装

devtools::install_local("C:\\Users\\admin\\Downloads\\SCENIC-master.zip")