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install.R
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install.R
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##
### ---------------
###
### Create: Jianming Zeng
### Date: 2019-07-24 15:03:19
### Email: [email protected]
### Blog: http://www.bio-info-trainee.com/
### Forum: http://www.biotrainee.com/thread-1376-1-1.html
### CAFS/SUSTC/Eli Lilly/University of Macau
### Update Log: 2019-07-24 First version
###
### ---------------
# 安装及加载必备的R包，耗时至少 1 小时+
# 这里需要 Seurat 是 3.0 的，如果版本不够，需要升级
if(F){
library(Seurat)
remove.packages('Seurat')
install.packages('Seurat')
library(Seurat)
}
library(ROTS)
library(Seurat)
library("matrixStats")
library("ggplot2")
library("Rtsne")
library("fpc")
library("factoextra")
library("monocle")
library("viridis")
library("gplots")
library("RColorBrewer")
library("destiny")
library("slingshot")
library("rgl")
library("scatterplot3d")
library("made4")
library("pheatmap")
library("matrixStats")
library("statmod")
library("FactoMineR")
library("jackstraw")
library("org.Mm.eg.db")
library("clusterProfiler")
library("GOSemSim")
library("arulesViz")
library("ggpubr")
options()$repos
options()$BioC_mirror
options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")
options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
options()$repos
options()$BioC_mirror
if(F){
#BiocManager::install("Seurat",ask = F,update = F)
BiocManager::install("monocle",ask = F,update = F)
BiocManager::install("destiny",ask = F,update = F)
BiocManager::install("slingshot",ask = F,update = F)
BiocManager::install("made4",ask = F,update = F)
BiocManager::install("lfa",ask = F,update = F)
BiocManager::install("ROTS",ask = F,update = F)
}
pkgs = c("taRifx"
,"matrixStats"
,"ggplot2"
,"Rtsne"
,"fpc"
,"factoextra"
,"monocle"
,"viridis"
,"gplots"
,"RColorBrewer"
,"destiny"
,"slingshot"
,"rgl"
,"scatterplot3d"
,"made4"
,"pheatmap"
,"matrixStats"
,"statmod"
,"FactoMineR"
,"jackstraw"
,"ReactomePA"
,"org.Mm.eg.db"
,"clusterProfiler"
,"GOSemSim"
,"arulesViz"
,"ggpubr")
# BiocManager::install(pkgs,ask = F,update = F)
###########################################
# #
# Load needed libraries #
# #
###########################################
library("taRifx")
library("matrixStats")
library("ggplot2")
library("Rtsne")
library("fpc")
library("factoextra")
library("monocle")
library("viridis")
library("gplots")
library("RColorBrewer")
library("destiny")
library("slingshot")
library("rgl")
library("scatterplot3d")
library("made4")
library("pheatmap")
library("matrixStats")
library("statmod")
library("FactoMineR")
library("jackstraw")
library("ReactomePA")
library("org.Mm.eg.db")
library("clusterProfiler")
library("GOSemSim")
library("arulesViz")
library("ggpubr")