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d3 = function() {
  var d3 = {
    version: "3.2.7"
  };
  if (!Date.now) Date.now = function() {
    return +new Date();
  };
  var d3_document = document, d3_documentElement = d3_document.documentElement, d3_window = window;
  try {
    d3_document.createElement("div").style.setProperty("opacity", 0, "");

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# RNA-seq: differential gene expression analysis

*[back to course contents](..)*

This is an introduction to RNAseq analysis involving reading in count data from an RNAseq experiment, exploring the data using base R functions and then analysis with the DESeq2 package.

## Install and load packages

First, we'll need to install some add-on packages. Most generic R packages are hosted on the Comprehensive R Archive Network (CRAN, <http://cran.us.r-project.org/>). To install one of these packages, you would use `install.packages("packagename")`. You only need to install a package once, then load it each time using `library(packagename)`. Let's install the **gplots** and **calibrate** packages.

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## See http://gettinggeneticsdone.blogspot.com/2013/06/customize-rprofile.html

## Load packages
library(BiocInstaller)

## Don't show those silly significanct stars
options(show.signif.stars=FALSE)

## Do you want to automatically convert strings to factor variables in a data.frame?
## WARNING!!! This makes your code less portable/reproducible.

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library(ganalytics)
library(plyr)
library(ggplot2)

###########################################
# Change profileId to your own GA profile #
###########################################
gaQuery <- GaQuery(profileId = 123456789) 

# Define our date range - end date is yesterday by default

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#### Demos in R
  ## see available demos by package
  demo(package = .packages(all.available = TRUE))

  
##### demos in 'HH'
  demo('likert-paper-noFormula', package='HH')
  demo('likert-paper',package="HH")
  demo(topic='likertMosaic-paper', package = "HH")
  

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# By default, the directories in .libPaths() aren't writable on shinyapps.io, so
# create a subdir where we'll install our package.
if (!file.exists("R-lib")) {
  dir.create("R-lib")
}
# Unfortunately, there's no way to get deployapp() to ignore this directory, so
# make sure to remove it locally before you call deployapp(). This can be done
# with:
#   unlink("pkgInst/R-lib", recursive = TRUE)

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* Reproducible Research  
  * Makefiles  
    * [Make for Reproducibility](http://zmjones.com/make/)  
    * [Why use Make](http://bost.ocks.org/mike/make/)  
    * [O'Reilly Make Book](http://oreilly.com/catalog/make3/book/)  
    * [Minimal Make, A Quick Tour](http://kbroman.org/minimal_make/)  
    * [Make for R and LaTeX](http://robjhyndman.com/hyndsight/makefiles/)
    * [Software Carpentry Make Lessons](http://software-carpentry.org/v4/make/index.html)
  * Misc
    * [Best Practices for Software and Reproducible Research](http://openresearchsoftware.metajnl.com/article/view/jors.ay/63)

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###############################################################################
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.

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R-Code
======

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require("shiny")
require("foreign")


#Then simply run:
shiny:::runGist("https://gist.github.com/SachaEpskamp/5796467")