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Further topics in R.

Building

To completely rebuild, type:

make clean ; make

On an older Ubuntu (eg 14), you might need to use the RStudio pandoc:

PATH=/usr/lib/rstudio-server/bin/pandoc:$PATH make

Dependencies

Command line software:

  • R
  • pandoc
  • java (Ubuntu: apt-get install default-jre)
  • fastqc

R packages:

install.packages(c(
    "readr",
    "tidyr",
    "dplyr",
    "ggplot2",
    "viridis",
    "broom",
    "shiny",
    "rmarkdown"
))

# To force a Bioconductor upgrade if you have an older version than 3.3:
try( remove.packages("BiocInstaller") )

source("https://bioconductor.org/biocLite.R")
biocLite()
biocLite(c(
    "Biostrings",
    "GenomicRanges",
    "BSgenome",
    "rtracklayer",
    "motifRG"
))

License

This material is made available under the Creative Commons Attribution 4.0 International License. See index.html for details.