Seurat R 安装及单细胞数据处理

1. … permission is denied.

Solution: Close R, and run it with administrator.

From: https://cloud.tencent.com/developer/article/1606588

2. Read Data

library(Seurat)
fs=list.files('./','^GSM')
library(stringr)
samples=str_split(fs,'_',simplify = T)[,1]
lapply(unique(samples),function(x){
  y=fs[grepl(x,fs)]
  folder=paste(str_split(y[1],'_',simplify = T)[,2:3],collapse = '')
  dir.create(folder,recursive = T)
  file.rename(y[1],file.path(folder,"barcodes.tsv.gz"))
  file.rename(y[2],file.path(folder,"genes.tsv.gz"))
  file.rename(y[3],file.path(folder,"matrix.mtx.gz"))
})

Then
unzip all files under the subfolders

ls */*gz|xargs  gunzip

folders=list.files('./')
folders
library(Seurat)
sceList = lapply(folders,function(folder){
    
  Creat