installer.r

In zhezhangsh/DEGandMore:

# Install dependency required to run the DE methods
installed <- rownames(installed.packages()); 

# Install required cran packages
pkg1 <- c('devtools', 'XML', 'readxl', 'shinythemes', 'GPseq', 'NBPSeq');
pkg  <- setdiff(pkg1, installed);
if (length(pkg) > 0) {
  install.packages(pkg); 
}
install_url("https://cran.r-project.org/src/contrib/Archive/multicore/multicore_0.2.tar.gz"); 

# install Bioconductor packages
pkg2 <- c("ABSSeq", "ALDEx2", "BADER", "ballgown", "baySeq", "BGmix", "bridge", "DEGseq", "DESeq2", "EBSeq", "edgeR", "edgeRun", 
          "limma", "LMGene", "metaseqR", "NOISeq", "plgem", "PoissonSeq", "RankProd", "RBM", "samr", "sSeq", "tweeDEseq"); 
pkg  <- setdiff(pkg2, installed);
if (length(pkg) > 0) {
  source("http://bioconductor.org/biocLite.R");
  biocLite(pkg); 
}
# Install older version, the newest version doesn't support paired test
install_url("https://www.bioconductor.org/packages/3.2/bioc/src/contrib/ABSSeq_1.6.1.tar.gz");

# install GitHub packages (force to install to keep)
pkg3 <- c('RoCA', 'rchive', 'awsomics', 'DEGandMore')
require(devtools); 
install_github('zhezhangsh/RoCAR');
install_github('zhezhangsh/rchive');
install_github('zhezhangsh/awsomicsR');
install_github('zhezhangsh/DEGandMore');

# install individual packages
#devtools::install_url("http://www.bios.unc.edu/research/genomic_software/BBSeq/index_files/BBSeq_3.0.zip");
install.packages(c("sp","pixmap", "snowfall", "VGAM", "mclust", "logcondens", "Iso","XML","rgl")); 
source("http://www.math.ntnu.no/inla/givemeINLA.R"); 
install_github("markvdwiel/ShrinkBayes"); 

# Check if all packages can be loaded
pkgs   <- c(pkg1, pkg2, pkg3); 
loaded <- sapply(pkgs, function(pkg) require(pkg, character.only = TRUE));
if(length(pkgs[!loaded]) == 0) cat("Congratulations! All required packages have been installed and loaded.\n") else
  cat('Oops!, Some packages are not installed/loaded: ', paste(pkgs[!loaded], collapse='; '), '\n');