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MEDIPS

Provides functions for the quality control and analysis of data derived from immunoprecipitation (IP)-seq samples. MEDIPS starts with the aligned reads (typically bam files) and can be used for any genome of interest. It allows for an arbitrary number of replicates per group and integrates sophisticated statistical methods for the detection of differential coverage between experimental conditions. This updated version 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.

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MEDIPS classification

MEDIPS specifications

Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
1.22.0
Requirements:
BSGenome, Rsamtools
Interface:
Command line interface
Input data:
It starts with the aligned reads (typically bam files) and can be used for any genome of interest.
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

MEDIPS distribution

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MEDIPS support

Documentation

Credits

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Publications

Institution(s)

Departments of Vertebrate Genomics and Developmental Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany; Department of Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany; Institute of Pathology, Laboratory of Molecular Tumour Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany; Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA

Funding source(s)

German Federal Ministry of Education and Research with the grant EPITREAT (No. 0316190A); the Max Planck Society with its International Research School program (IMPRS-CBSC); Feodor Lynen postdoctoral Research Fellowship from the Alexander von Humboldt Foundation

Link to literature

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