Biocbrazil2014

Overview

Code and vignettes in support of the SummerX Bioconductor course in Brazil

Introduction to the ExpressionSet

Paste this into R to download the materials:

download.file('http://seandavi.github.io/BiocBrazil2014/vignettes/ExpressionSetSlides.Rnw',
    destfile='ExpressionSetSlides.Rnw')
download.file('http://seandavi.github.io/BiocBrazil2014/vignettes/ExpressionSetSlides.pdf',
    destfile='ExpressionSetSlides.pdf')
download.file('http://seandavi.github.io/BiocBrazil2014/vignettes/ExpressionSetSlides.R',
    destfile='ExpressionSetSlides.R')

Links below can be used to download by hand:

• ExpressionSetSlides.pdf
• ExpressionSetSlides.R
• ExpressionSetSlides.Rnw

Variant Exercises

Paste this into R to download the materials:

source('http://seandavi.github.io/BiocBrazil2014/downloadfile.R')

Links below can be used to download by hand:

• VariantsExercises.pdf
• VariantsExercises.R
• VariantsExercises.Rnw

Differential Expression Analysis with DESeq2

Paste this into R to download the materials:

download.file('http://seandavi.github.io/BiocBrazil2014/vignettes/DESeq2_parathyroid.pdf',
    destfile='DESeq2_parathyroid.pdf')
download.file('http://seandavi.github.io/BiocBrazil2014/vignettes/DESeq2_parathyroid.R',
    destfile='DESeq2_parathyroid.R')

Links below can be used to download by hand:

• DESeq2_parathyroid.pdf
• DESeq2_parathyroid.R
• DESeq2_parathyroid.Rnw

Processing 450k Methylation Data with the minfi Package

Paste this into R to download the materials:

download.file('http://seandavi.github.io/BiocBrazil2014/vignettes/minfi.pdf',
    destfile='minfi.pdf')
download.file('http://seandavi.github.io/BiocBrazil2014/vignettes/minfi.R',
    destfile='minfi.R')

Links below can be used to download by hand:

• minfi.pdf
• minfi.R
• minfi.Rnw