packages.R

# For all weeks:

install.packages("devtools")
library(devtools)
install_github("ririzarr/rafalib")
install_github("genomicsclass/dagdata")

source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("Biobase")
biocLite("GenomicRanges")

# Week 1

install.packages("dplyr")
biocLite("Biobase")

# Week 2

biocLite("GEOquery")
biocLite("parathyroidSE")
install.packages("matrixStats")
install.packages("RColorBrewer")
biocLite("affy")
biocLite("oligo")

# Week 3

biocLite("genefilter")
biocLite("limma")
install.packages("animation")

# Week 4

biocLite("SpikeInSubset")
library(devtools);install_github("BackgroundExperimentYeast","stephaniehicks")
biocLite("SpikeIn")
install.packages("MASS")
biocLite("parathyroidSE")
install.packages("matrixStats")
biocLite("limma")
biocLite("affy")
install.packages("animation")
biocLite("preprocessCore")
biocLite("vsn")
library(devtools);install_github("mycAffyData","stephaniehicks")
install.packages("SQN")

# Week 5

install.packages("class")
install.packages("caret")
install.packages("RColorBrewer")
biocLite("genefilter")
install.packages("gplots")
install.packages("matrixStats")
install.packages("animation")
biocLite("yeastCC")
install.packages("UsingR")

# Week 6
 
biocLite("genefilter")
install.packages("MASS")
biocLite("hgfocus.db")
biocLite("sva")
biocLite("limma")

# Week 7

biocLite("GEOquery")
biocLite("limma")
biocLite("org.Hs.eg.db")
biocLite("GO.db")
biocLite("SpikeInSubset")
biocLite("genefilter")
biocLite("rae230a.db")
biocLite("AnnotationDbi")
biocLite("biomaRt")

# Week 8

biocLite("pasillaBamSubset")
biocLite("TxDb.Dmelanogaster.UCSC.dm3.ensGene")
biocLite("Rsamtools")
biocLite("GenomicAlignments")
biocLite("DESeq2")
biocLite("biomaRt")
biocLite("Gviz")
biocLite("ggbio")

# For building data objects

biocLite("GEOquery")
biocLite("affy")
biocLite("simpleaffy")
biocLite("SpikeIn")