R包安装的正确方式
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))
注：本文转自“生信技能树”
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