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

可进官网查询

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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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