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Installation of most R packages I use
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| # Bioconductor packages | |
| source("http://bioconductor.org/biocLite.R") | |
| biocLite(ask=FALSE) | |
| biocLite(c("preprocessCore", "biomaRt", "affy", "limma", "beadarray", "ggplot2", "impute", "DESeq2", "Rsamtools", "vsn")) | |
| biocLite(c("topGO", "GO.db", "KEGG.db", "MotifDb", "seqLogo", "motifStack")) | |
| biocLite(c("Biostrings", "GenomicAlignments", "GenomicFeatures", "BiocParallel")) | |
| biocLite(c("BSgenome.Mmusculus.UCSC.mm10", "TxDb.Mmusculus.UCSC.mm10.ensGene")) | |
| biocLite(c("gcrma", "lumi", "ShortRead", "cdfpackage", "seqinr", "reshape2", "plyr", "scales")) | |
| # CRAN packages | |
| install.packages("ape") | |
| install.packages("devtools") | |
| install.packages("extrafont") | |
| install.packages("qtl") | |
| install.packages("qtlDesign") | |
| install.packages("randomForest") | |
| install.packages("rJava") | |
| install.packages("pheno2geno") | |
| install.packages("plotrix") | |
| install.packages("RCurl") | |
| install.packages("WGCNA") | |
| install.packages("snow") | |
| install.packages("nlme") | |
| install.packages("lme4") | |
| install.packages("xlsx") | |
| install.packages("psych") | |
| install.packages("GPArotation") |
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