安装TCGA挖掘所需R包

### Create: Jianming Zeng
### Date: 2019-04-02 21:59:01
### Email: jmzeng1314@163.com
### Blog: http://www.bio-info-trainee.com/
### Forum:  http://www.biotrainee.com/thread-1376-1-1.html

rm(list = ls()) 
#清空当前工作空间变量  
options()$repos  
#查看当前工作空间默认的下载包路径
options()$BioC_mirror 
#查看使用BioCManager下载包的默认路径
options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/") 
# 指定使用BioCManager下载的路径
options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/")) 
# 指定使用install.packages下载包的路径
options()$repos 
options()$BioC_mirror


# https://bioconductor.org/packages/release/bioc/html/GEOquery.html
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")  #BiocManager是安装bioconductor相关包的基础包

#判断是否存在这些包，不存在的话安装这些包
if(!require("KEGG.db")) BiocManager::install("KEGG.db",ask = F,update = F)
if(!require("GSEABase")) BiocManager::install("GSEABase",ask = F,update = F)
if(!require("GSVA")) BiocManager::install("GSVA",ask = F,update = F)
if(!require("clusterProfiler")) BiocManager::install("clusterProfiler",ask = F,update = F)
if(!require("GEOquery")) BiocManager::install("GEOquery",ask = F,update = F)
if(!require("limma")) BiocManager::install("limma",ask = F,update = F)
if(!require("impute")) BiocManager::install("impute",ask = F,update = F)
if(!require("genefu")) BiocManager::install("genefu",ask = F,update = F)
if(!require("org.Hs.eg.db")) BiocManager::install("org.Hs.eg.db",ask = F,update = F)
if(!require("hgu133plus2.db")) BiocManager::install("hgu133plus2.db",ask = F,update = F)
if(!require("ConsensusClusterPlus")) BiocManager::install("ConsensusClusterPlus",ask = F,update = F)
# BiocManager::install(c('airway','DESeq2','edgeR','limma'),ask = F,update = F)
if(!require("airway")) BiocManager::install("airway",ask = F,update = F)
if(!require("DESeq2")) BiocManager::install("DESeq2",ask = F,update = F)
if(!require("edgeR")) BiocManager::install("edgeR",ask = F,update = F)
if(!require("limma")) BiocManager::install("limma",ask = F,update = F)

if(! require("maftools")) BiocManager::install("maftools",ask = F,update = F)
if(! require("genefilter")) BiocManager::install("genefilter",ask = F,update = F)

if(! require("CLL")) BiocManager::install("CLL",ask = F,update = F)
if(! require("org.Hs.eg.db")) BiocManager::install('org.Hs.eg.db',ask = F,update = F)

if(! require("maftools")) BiocManager::install("maftools",ask = F,update = F)
if(! require("RTCGA")) BiocManager::install("RTCGA",ask = F,update = F)
if(! require("RTCGA.clinical")) BiocManager::install("RTCGA.clinical",ask = F,update = F)
# https://bioconductor.org/packages/3.6/data/experiment/src/contrib/RTCGA.clinical_20151101.8.0.tar.gzn
if(! require("RTCGA.miRNASeq")) BiocManager::install("RTCGA.miRNASeq",ask = F,update = F)

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