周末生物信息学培训班准备工作

第一个准备工作是安装必备软件：

• 腾讯微云链接:https://share.weiyun.com/5hW6VAA 密码 : d63d2c
• 百度云：链接:https://pan.baidu.com/s/1v4tw9cmhnr3bTr1EOAKfwA 密码:vp96

其中R和Rstudio安装后，需要打开rstudio，然后安装一些R包，如下：

尽可能的听完我在B站的R语言课程哈，链接是：https://www.bilibili.com/video/av25643438/

R包安装

rm(list = ls())   
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("genefu","org.Hs.eg.db","hgu133plus2.db" ),ask = F,update = F)


# 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"))

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(genefu)
library(ggplot2)
library(ggpubr)
library(hgu133plus2.db)
library(limma)
library(org.Hs.eg.db)
library(pheatmap)

初学者安装R包遇到报错非常正常，所以才需要培训，部分报错的解决方案见：https://docs.qq.com/doc/DT2VMdmN2Y0F5SHlr