Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia
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README.md
analyse.R
process_annotations.R
process_geneexpression.R
process_intensities.R
process_methylation.R
process_phenotypes.R
setup.R

README.md

Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia

Nordlund J, Bäcklin C, Wahlberg P, Busche S, Berglund EC, Eloranta M-L, Flaegstad T, Forestier E, Frost B-M, Harila-Saari A, Heyman M, Jónsson OG, Larsson R, Palle J, Rönnblom L, Schmiegelow K, Sinnett D, Söderhäll S, Pastinen T, Gustafsson MG, Lönnerholm G & Syvänen AC

Original publication: Genome Biology 2013, 14:r105

This code was produced by the groups of Molecular Medicine and Cancer Pharmacology and Computational Medicine at the Department of Medical Sciences at Uppsala University.

System requirements

R version 2.15.3 or later. Packages plyr and GEOquery are required, but are installed automatically.

Parallelization using the foreach and doSNOW packages is recommended, but not required.

Figures were annotated using the biomaRt and GenomeGraphs packages. However, code for producing the figures is not included.

Instructions

Download all scripts in this repo to a new directory. The most convenient way to do this on a linux/unix system is to clone the whole repo. Then run the files setup.R and analyse.R.

git clone git@github.com:Molmed/Nordlund-Backlin-2013.git
cd Nordlund-Backlin-2013
R -f setup.R
R -f analyse.R

setup.R will download all data from GEO, prepare it for use in R and store it in a new subfolder called data. analyse.R will run the analyses, produce the results and save them in a new subfolder called results. Plots are not produced.