Note that these instructions will be updated based on participants' feedback.
Last update: Mon Feb 10 21:19:23 2020
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.
To install all requirements, please copy and paste this line of code in your R console.
source("https://uclouvain-cbio.github.io/BSS2020/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.
message("* Checking R version.")## * Checking R version.stopifnot(base::version$major == "3")
stopifnot(base::version$minor >= "6.2")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## Bioconductor version 3.10 (BiocManager 1.30.10), ?BiocManager::install for helpBelow 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" "affyio"
## [3] "apeglm" "Biobase"
## [5] "BiocGenerics" "BiocManager"
## [7] "BiocParallel" "biomaRt"
## [9] "Biostrings" "BSgenome"
## [11] "BSgenome.Hsapiens.UCSC.hg38" "ca"
## [13] "class" "colorspace"
## [15] "curatedTCGAData" "DESeq2"
## [17] "dichromat" "doParallel"
## [19] "dplyr" "DT"
## [21] "edgeR" "EnrichmentBrowser"
## [23] "fdrtool" "foreach"
## [25] "GenomicAlignments" "GenomicFeatures"
## [27] "GenomicRanges" "ggbeeswarm"
## [29] "ggplot2" "GO.db"
## [31] "graphics" "grDevices"
## [33] "gtable" "htmltools"
## [35] "htmlwidgets" "httpuv"
## [37] "impute" "IRanges"
## [39] "iSEE" "ISLR"
## [41] "iterators" "KEGGREST"
## [43] "labeling" "lazyeval"
## [45] "limma" "lme4"
## [47] "magrittr" "MALDIquant"
## [49] "MASS" "Matrix"
## [51] "methods" "miniUI"
## [53] "minqa" "msdata"
## [55] "MSnbase" "MultiAssayExperiment"
## [57] "munsell" "mzID"
## [59] "mzR" "nloptr"
## [61] "numDeriv" "openxlsx"
## [63] "org.Hs.eg.db" "pcaMethods"
## [65] "pheatmap" "plyr"
## [67] "preprocessCore" "ProtGenerics"
## [69] "RColorBrewer" "Rcpp"
## [71] "reshape2" "rjson"
## [73] "rmarkdown" "rmdformats"
## [75] "rtracklayer" "scales"
## [77] "shiny" "shinydashboard"
## [79] "shinyFiles" "shinyjs"
## [81] "shinythemes" "SingleCellExperiment"
## [83] "snow" "statmod"
## [85] "statOmics/MSqRob" "stringi"
## [87] "stringr" "SummarizedExperiment"
## [89] "svDialogs" "tibble"
## [91] "tidyr" "tidyverse"
## [93] "TxDb.Hsapiens.UCSC.hg38.knownGene" "tximeta"
## [95] "utils" "vsn"
## [97] "XML" "xtable"
## [99] "yaml" "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 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12)## Installation path not writeable, unable to update packages: foreign, nlmeThe
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")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.