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  MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments

Lienhard, M., Grimm, C., Morkel, M., Herwig, R., & Chavez, L. (2014). MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. Bioinformatics, 30(2), 284-286. doi:10.1093/bioinformatics/btt650.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002A-6115-E Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002A-6116-C
Genre: Journal Article

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 Creators:
Lienhard, Matthias1, Author              
Grimm, Christina2, Author              
Morkel, Markus3, Author              
Herwig, Ralf1, Author              
Chavez, Lukas4, Author              
Affiliations:
1Bioinformatics (Ralf Herwig), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479648              
2In vitro Ligand Screening (Zoltán Konthur), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479653              
3Dept. of Developmental Genetics (Head: Bernhard G. Herrmann), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433548              
4Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              

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 Abstract: MOTIVATION: 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. AVAILABILITY AND IMPLEMENTATION: 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.

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Language(s): eng - English
 Dates: 2013-10-262013-11-042013-11-132014-01-15
 Publication Status: Published in print
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 Identifiers: Other: accessionPMC3892689
Other: pmcidPMC3892689
Other: pmc-uid3892689
PMID: 24227674
DOI: 10.1093/bioinformatics/btt650
Other: publisher-idbtt650
URI: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3892689&tool=pmcentrez&rendertype=abstract
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Funding organization : German Federal Ministry of Education and Research with the grant EPITREAT (No. 0316190A) and by the Max Planck Society with its International Research School program (IMPRS-CBSC). Feodor Lynen postdoctoral Research Fellowship from the Alexander von Humboldt Foundation (to L.C.

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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford University Press
Pages: - Volume / Issue: 30 (2) Sequence Number: - Start / End Page: 284 - 286 Identifier: Other: Bioinformatics
Other: Bioinformatics
Other: bioinformatics
Other: bioinfo
ISSN: 1367-4803
ISSN: 1367-4811