MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments.
BACKGROUND
DNA enrichment followed by sequencing is a versatile tool in molecular biology, with a wide variety of applications including genome-wide analysis of epigenetic marks and mechanisms. A common requirement of these diverse applications is a comparison of read coverage between experimental conditions. The amount of samples generated for such comparisons ranges from few replicates to hundreds of samples per condition for epigenome-wide association studies. Consequently, there is an urgent need for software that allows for fast and simple processing and comparison of sequencing data derived from enriched DNA.


RESULTS
Here, we present a major update of the R/Bioconductor package MEDIPS, which allows for an arbitrary number of replicates per group and integrates sophisticated statistical methods for the detection of differential coverage between experimental conditions. Our approach can be applied to a diversity of quantitative sequencing data. In addition, our update adds novel functionality to MEDIPS, including correlation analysis between samples, and takes advantage of Bioconductor's annotation databases to facilitate annotation of specific genomic regions.


METHODS
The latest version of MEDIPS is available as version 1.12.0 and part of Bioconductor 2.13. The package comes with a manual containing detailed description of its functionality and is available at http://www.bioconductor.org.
Departments of Vertebrate Genomics and Developmental Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany, Department of Rheumatology and Clinical Immunology, Institute of Pathology, Laboratory of Molecular Tumour Pathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany and Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
Matthias
M
Lienhard
Christina
C
Grimm
Markus
M
Morkel
Ralf
R
Herwig
Lukas
L
Chavez
D000236:Adenoma / Q000235:genetics; D000818:Animals; D047369:Chromatin Immunoprecipitation; D018899:CpG Islands; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000378:metabolism; D016208:Databases, Factual; D057890:Epigenomics; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods*; D007414:Intestinal Neoplasms / Q000235:genetics; D051379:Mice; D011786:Quality Control; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D004268:DNA-Binding Proteins; C489323:Mbd1 protein, mouse