下游分析軟件：https://github.com/ZilongZhang44/single-cell-downstream-analysis

#設置R包默認安裝鏡像：

options(repos=structure(c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))) 

#安裝biocmanager包
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install(version = "3.12")
#調用biocmanager包
library("BiocManager")
#利用biomanager安裝常用的包
BiocManager::install(c("ggplot2","ggtree","DESeq2"))

#安裝seurat
install.packages("Seurat",dependencies=T)
library(Seurat)
#查看Seurat版本信息
packageVersion("Seurat")
# 安裝scran
# library(BiocManager)
BiocManager::install("scran")
library(scran)
# 詳細展示分群的分辨率
install.packages('clustree')
library(clustree)
#安裝devtools
install.packages("devtools",dependencies=T)
library("devtools")
#安裝SingleR\cellassign
library(devtools)
devtools::install_github("LTLA/SingleR")
BiocManager::install("SingleR") # 上述安裝報錯，可以使用這種安裝方式
library(SingleR)
# install.packages("tensorflow")
# tensorflow::install_tensorflow(extra_packages='tensorflow-probability', version = "2.1.0")

#安裝clusterProfiler
BiocManager::install("clusterProfiler")
library(clusterProfiler)
#安裝Monocle2和Monocle3包；
BiocManager::install("monocle",force = TRUE)
library(monocle)
# package.version(monocle)
#利用biomanager安裝常用的包
BiocManager::install(c("dplyr","BiocParallel",'scater','SummarizedExperiment'),force = TRUE)
#安裝Italk
## Download and install the package
install.packages("igraph")

## Load package
library(igraph)

if(!require(devtools)) 
  install.packages("devtools")
devtools::install_github("Coolgenome/iTALK", build_vignettes = TRUE)
library(iTALK)
remotes::install_github("Coolgenome/iTALK", build_vignettes = TRUE)
devtools::install_github("sqjin/CellChat")
library(CellChat)
# 安裝DoubletFinder
install.packages("remotes")
library(remotes)
remotes::install_github('chris-mcginnis-ucsf/DoubletFinder')

# 安裝傳參的包
install.packages("getopt")
# remotes:install_github("trevorld/r-getopt")
# https://www.cnblogs.com/timeisbiggestboss/p/7811009.html
install.packages("optparse")
remotes::install_github("trevorld/r-optparse")

# 安裝數(shù)據(jù)標準化包
devtools::install_github(repo = 'ChristophH/sctransform')