单细胞分析基础-第一节 数据质控、降维聚类

scRNA_pipeline\1.Seurat 生物技能树

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分析流程

准备：R包安装

options("repos"="https://mirrors.ustc.edu.cn/CRAN/")
if(!require("BiocManager")) install.packages("BiocManager",update = F,ask = F)
options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")#可改为西湖大学的镜像，如下

options(BioC_mirror="https://mirrors.westlake.edu.cn/bioconductor")


cran_packages <- c('tidyverse',
                   'msigdbr',
                   'patchwork',
                   'SeuratObject',
                   'Seurat'
                   ) 
Biocductor_packages <- c('sva',
                         'monocle',
                         'GOplot',
                         'GSVA',
                         'plotmo',
                         'regplot',
                         'scRNAseq',
                         'BiocStyle',
                         'celldex',
                         'SingleR',
                         'BiocParallel'
)

for (pkg in cran_packages){
   
  if (! require(pkg,character.only=T,quietly = T) ) {
   
    install.packages(pkg,ask = F,update = F)
    require(pkg,character.only=T) 
  }
}


for (pkg in Biocductor_packages){
   
  if (! require(pkg,character.only=T,quietly = T) ) {
   
    BiocManager::install(pkg,ask = F,update = F)
    require(pkg,character.only=T) 
  }
}

for (pkg in c(Biocductor_packages,cran_packages)){
   
  require(pkg,character.only=T) 
}

packageVersion("Seurat")
devtools::install_github( 'immunogenomics/presto')

分析流程

1.数据和R包准备

代码：https://satijalab.org/seurat/articles/pbmc3k_tutorial
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