单细胞分析常用包

安装基础包

install.packages("devtools", dependencies=T)
install.packages("BiocManager", dependencies=T)
install.packages("tidyverse", dependencies=T)
install.packages('Seurat', dependencies=T)

设置国内镜像

options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor/")
options("repos" = c(CRAN="http://mirrors.cloud.tencent.com/CRAN/"))
options(download.file.method = 'libcurl')
options(url.method='libcurl')

使用BiocManager安装分析包

BiocManager::install(c("SingleR","monocle", "DESeq2"),ask = F,update = F)
BiocManager::install(c("clusterProfiler","DOSE","pheatmap"),ask = F,update = F)
BiocManager::install(c("org.Hs.eg.db","org.Mm.eg.db","org.Rn.eg.db"),ask = F,update = F)
BiocManager::install("MAST")