生信技能树学习之入门武器装备

1. 入门软件安装
   everything
   Xshell
   git
   R
   RStudio
   typora
   winSCP

2. R包安装
   代码源于“生信菜鸟团”：

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

# https://bioconductor.org/packages/release/bioc/html/GEOquery.html
if (!requireNamespace("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("KEGG.db",ask = F,update = F)
BiocManager::install(c("GSEABase","GSVA","clusterProfiler" ),ask = F,update = F)
BiocManager::install(c("GEOquery","limma","impute" ),ask = F,update = F)
BiocManager::install(c("org.Hs.eg.db","hgu133plus2.db" ),ask = F,update = F)

# 下面代码被我注释了，意思是这些代码不需要运行，因为它过时了，很多旧教程就忽略
# 在代码前面加上 # 这个符号，代码代码被注释，意思是不会被运行
# source("https://bioconductor.org/biocLite.R") 
# library('BiocInstaller') 
# options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/") 
# BiocInstaller::biocLite("GEOquery")
# BiocInstaller::biocLite(c("limma"))
# BiocInstaller::biocLite(c("impute"))

# 但是接下来的代码又需要运行啦
options()$repos
install.packages('WGCNA')
install.packages(c("FactoMineR", "factoextra"))
install.packages(c("ggplot2", "pheatmap","ggpubr"))
library("FactoMineR")
library("factoextra")

library(GSEABase)
library(GSVA)
library(clusterProfiler)
library(ggplot2)
library(ggpubr)
library(hgu133plus2.db)
library(limma)
library(org.Hs.eg.db)
library(pheatmap)