Installation instructions

Note that these instructions will be updated based on participants' feedback.

Last update: Mon Jul 1 07:08:30 2019

Software and hardware requirement

Participants are required to bring their own laptop with R version 3.6.0 or greater. We also recommend to also install the latest version of RStudio.

Please make sure that your computer’s hardware is sufficiently powered (>4 GB RAM, > 2 GB free disk space), that you have a working wireless card, and that you have administrator rights.

Installation script

To install all requirements, please copy and paste this line of code in your R console.

source("https://uclouvain-cbio.github.io/BSS2019/installation.R")

The whole installation can take some time, if many of the required packages aren't already installed. At the end, you should see a Success! message, indicating that all dependencies are installed and up-to-date, and you will also have the airway.zip and extdata.zip files in your working directory.

The rest of this page describes the content of the installation script executed with the above line. It is given for information. In case of installation issues, check you internet connection and try to run the script a second time. If problems persist, please send your questions to the summer school mailing list, or try to execute the installation steps below one by one.

R version

message("* Checking R version.")
## * Checking R version.
stopifnot(base::version$major == "3")
stopifnot(base::version$minor >= "6.0")

Package installation

We are going to user the BiocManager package to install all other packages from the CRAN and Bioconductor repositories. Let's start by installing BiocManager if it's not already available:

message("* Installing BiocManager.")
## * Installing BiocManager.
if (!require("BiocManager"))
    install.packages("BiocManager")
## Loading required package: BiocManager

Below is a vector containing the names of all required packages:

pkgs <- c("rjson", "shinydashboard", "shiny", "shinyjs",
          "shinythemes", "shinyFiles", "openxlsx", "statOmics/MSqRob",
          "iSEE", "SummarizedExperiment", "SingleCellExperiment",
          "tximeta", "org.Hs.eg.db", "DESeq2", "edgeR", "pheatmap",
          "rmdformats", "apeglm", "lme4", "tidyverse", "rmarkdown",
          "Biobase", "DT", "fdrtool", "graphics", "grDevices",
          "limma", "MASS", "Matrix", "methods", "MSnbase", "numDeriv",
          "openxlsx", "plyr", "preprocessCore", "statmod", "msdata",
          "svDialogs", "utils", "vsn", "miniUI", "htmltools", "mzR",
          "ProtGenerics", "BiocParallel", "snow", "httpuv", "xtable",
          "htmlwidgets", "colorspace", "RColorBrewer", "dichromat",
          "munsell", "labeling", "affyio", "zlibbioc", "doParallel",
          "gtable", "scales", "tibble", "lazyeval", "reshape2",
          "affy", "impute", "pcaMethods", "mzID", "MALDIquant",
          "ggplot2", "XML", "minqa", "nloptr", "magrittr", "yaml",
          "stringr", "stringi", "foreach", "iterators", "Rcpp",
          "BiocGenerics", "BiocManager", "biomaRt", "Biostrings",
          "BSgenome", "BSgenome.Hsapiens.UCSC.hg38", "ggbeeswarm",
          "ISLR", "ca", "class", "curatedTCGAData", "dplyr",
          "EnrichmentBrowser", "GenomicAlignments", "GenomicFeatures",
          "GenomicRanges", "ggplot2", "GO.db", "IRanges", "KEGGREST",
          "MultiAssayExperiment", "org.Hs.eg.db", "rtracklayer",
          "limma", "SingleCellExperiment", "SummarizedExperiment",
          "tibble", "tidyr", "TxDb.Hsapiens.UCSC.hg38.knownGene")
pkgs <- sort(unique(pkgs))
pkgs
##   [1] "affy"                             
##   [2] "affyio"                           
##   [3] "apeglm"                           
##   [4] "Biobase"                          
##   [5] "BiocGenerics"                     
##   [6] "BiocManager"                      
##   [7] "BiocParallel"                     
##   [8] "biomaRt"                          
##   [9] "Biostrings"                       
##  [10] "BSgenome"                         
##  [11] "BSgenome.Hsapiens.UCSC.hg38"      
##  [12] "ca"                               
##  [13] "class"                            
##  [14] "colorspace"                       
##  [15] "curatedTCGAData"                  
##  [16] "DESeq2"                           
##  [17] "dichromat"                        
##  [18] "doParallel"                       
##  [19] "dplyr"                            
##  [20] "DT"                               
##  [21] "edgeR"                            
##  [22] "EnrichmentBrowser"                
##  [23] "fdrtool"                          
##  [24] "foreach"                          
##  [25] "GenomicAlignments"                
##  [26] "GenomicFeatures"                  
##  [27] "GenomicRanges"                    
##  [28] "ggbeeswarm"                       
##  [29] "ggplot2"                          
##  [30] "GO.db"                            
##  [31] "graphics"                         
##  [32] "grDevices"                        
##  [33] "gtable"                           
##  [34] "htmltools"                        
##  [35] "htmlwidgets"                      
##  [36] "httpuv"                           
##  [37] "impute"                           
##  [38] "IRanges"                          
##  [39] "iSEE"                             
##  [40] "ISLR"                             
##  [41] "iterators"                        
##  [42] "KEGGREST"                         
##  [43] "labeling"                         
##  [44] "lazyeval"                         
##  [45] "limma"                            
##  [46] "lme4"                             
##  [47] "magrittr"                         
##  [48] "MALDIquant"                       
##  [49] "MASS"                             
##  [50] "Matrix"                           
##  [51] "methods"                          
##  [52] "miniUI"                           
##  [53] "minqa"                            
##  [54] "msdata"                           
##  [55] "MSnbase"                          
##  [56] "MultiAssayExperiment"             
##  [57] "munsell"                          
##  [58] "mzID"                             
##  [59] "mzR"                              
##  [60] "nloptr"                           
##  [61] "numDeriv"                         
##  [62] "openxlsx"                         
##  [63] "org.Hs.eg.db"                     
##  [64] "pcaMethods"                       
##  [65] "pheatmap"                         
##  [66] "plyr"                             
##  [67] "preprocessCore"                   
##  [68] "ProtGenerics"                     
##  [69] "RColorBrewer"                     
##  [70] "Rcpp"                             
##  [71] "reshape2"                         
##  [72] "rjson"                            
##  [73] "rmarkdown"                        
##  [74] "rmdformats"                       
##  [75] "rtracklayer"                      
##  [76] "scales"                           
##  [77] "shiny"                            
##  [78] "shinydashboard"                   
##  [79] "shinyFiles"                       
##  [80] "shinyjs"                          
##  [81] "shinythemes"                      
##  [82] "SingleCellExperiment"             
##  [83] "snow"                             
##  [84] "statmod"                          
##  [85] "statOmics/MSqRob"                 
##  [86] "stringi"                          
##  [87] "stringr"                          
##  [88] "SummarizedExperiment"             
##  [89] "svDialogs"                        
##  [90] "tibble"                           
##  [91] "tidyr"                            
##  [92] "tidyverse"                        
##  [93] "TxDb.Hsapiens.UCSC.hg38.knownGene"
##  [94] "tximeta"                          
##  [95] "utils"                            
##  [96] "vsn"                              
##  [97] "XML"                              
##  [98] "xtable"                           
##  [99] "yaml"                             
## [100] "zlibbioc"

We first check which packages are already available, update all old packages with the latest available versions and proceed with the installation of packages that aren't installed yet.

message("* Installing packages.")
## * Installing packages.
ip <- rownames(installed.packages())
pkgs_to_install <- pkgs[which(!sub("^.+/", "", pkgs) %in% ip)]
BiocManager::install(pkgs_to_install, update = TRUE, ask = FALSE, upgrade = 'always')
## Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 RC (2019-04-21
##   r76417)

Download additional data

The airway.zip file contains data that will be used during the RNASeq sessions. It can be downloaded from R in the working directory with:

message("* Downloading data.")
## * Downloading data.
download.file("https://uclouvain-cbio.github.io/BSS2019/airway.zip", "airway.zip")
download.file("https://uclouvain-cbio.github.io/BSS2019/extdata.zip", "extdata.zip")

Success

If you see the following message in your console, it means you have successfully installed all requirements.

message("* Success!")
## * Success!

Back to the summer school page.