- 1 options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
- 2 if(! require("devtools")) install.packages("devtools")
- 3 if(! require("reshape2")) install.packages("reshape2")
- 4 if(! require("ggplot2")) install.packages("ggplot2")
- 5 if(! require("pheatmap")) install.packages("pheatmap")
- 6 if(! require("ggfortify")) install.packages("ggfortify")
- 7 if(! require("stringr")) install.packages("stringr")
- 8 if(! require("survival")) install.packages("survival")
- 9 if(! require("survminer")) install.packages("survminer")
- 10 if(! require("lars")) install.packages("lars")
- 11 if(! require("glmnet")) install.packages("glmnet")
- 12
- 13 if(! require("timeROC")) install.packages("timeROC")
- 14 if(! require("ggpubr")) install.packages("ggpubr")
- 15
- 16 if(! require("randomForest")) install.packages("randomForest")
- 17 if(! require("ROCR")) install.packages("ROCR")
- 18 if(! require("Hmisc")) install.packages("Hmisc")
- 19
- 20 if(! require("caret")) install.packages("caret")
- 21 # if(! require("genefilter")) install.packages("genefilter")
- 22 if(! require("ggstatsplot")) install.packages("ggstatsplot")
- 23
- 24 ### 下面的包是为了临床三线表
- 25 if(! require("tableone")) install.packages("tableone")
- 26 ## 网络不好,就不要安装了。
- 27 ## 而且Windows电脑安装 rJava 也经常是需要人指导的。
- 28 # https://github.com/rstudio/rstudio/issues/2254
- 29 if(! require("rJava")) install.packages("rJava")
- 30 if(require('rJava')){
- 31
- 32 # https://cran.r-project.org/src/contrib/Archive/ReporteRs/
- 33 if(! require("ReporteRs")) install.packages("ReporteRs")
- 34 devtools::install_github('davidgohel/ReporteRsjars')
- 35 devtools::install_github('davidgohel/ReporteRs')
- 36 }
- 37
- 38
- 39 library(devtools)
- 40 source("http://bioconductor.org/biocLite.R")
- 41 ## 如果你的网络实在是太差,试试看:
- 42 # install.packages("BiocInstaller",repos="http://bioconductor.org/packages/3.7/bioc")
- 43 ## 很可惜你在中国大陆,不得不承受这个痛苦。
- 44
- 45 options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")
- 46 library('BiocInstaller')
- 47 if(! require('edgeR')){
- 48
- 49 biocLite(c('airway','DESeq2','edgeR','limma'))
- 50 }
- 51
- 52 if(! require("CLL")) biocLite("CLL")
- 53 if(! require("org.Hs.eg.db")) biocLite('org.Hs.eg.db')
- 54 library(BiocInstaller)
- 55 options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")
- 56 if(! require("maftools")) biocLite("maftools")
- 57 if(! require("RTCGA")) biocLite("RTCGA")
- 58 if(! require("RTCGA.clinical")) biocLite("RTCGA.clinical")
- 59 # https://bioconductor.org/packages/3.6/data/experiment/src/contrib/RTCGA.clinical_20151101.8.0.tar.gzn
- 60 if(! require("RTCGA.miRNASeq")) biocLite("RTCGA.miRNASeq")
- 61 if(! require("maftools")) biocLite("maftools")
- 62 if(! require("genefilter")) biocLite("genefilter")
- 63
- 64
- 65 # Then from : https://github.com/ShixiangWang
- 66 # You don't need run the codes below, I will explain to you face to face.
- 67
- 68 source("http://bioconductor.org/biocLite.R")
- 69 packs = c("devtools", "reshape2", "ggplot2", "pheatmap", "ggfortify", "stringr", "survival",
- 70 "survminer", "lars", "glmnet", "timeROC", "ggpubr", "randomForest", "ROCR", "genefilter",
- 71 "Hmisc", "caret", "airway","DESeq2","edgeR","limma", "CLL", "org.Hs.eg.db", "maftools")
- 72 if(! require(pacman)) install.packages("pacman", dependencies = TRUE)
- 73 pacman::p_load(packs, dependencies=TRUE, character.only = TRUE)
- 74 # check
- 75 pacman::p_loaded(packs, character.only = TRUE)
- 76 all(pacman::p_loaded(packs, character.only = TRUE))
- https://mp.weixin.qq.com/s?__biz=MzAxMDkxODM1Ng==&mid=2247487157&idx=1&sn=0540a2788eba7b5a96a6d4f907d92718&chksm=9b484e0eac3fc71864f0e1d5959ac5f768bd3289312c2d0776cbe663a888edd056b092175d5c&mpshare=1&scene=23&srcid=0809lYoGGKt6uOM4j8rCH40P#rd