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DChIPRep

Compares profiles of enrichment in histone modifications around classes of genomic elements, e.g. transcription start sites (TSS). DChIPRep tests for differential enrichment at each nucleotide position of a metagene/metafeature profile and determines positions with significant differences in enrichment between experimental groups. DChIPRep provides two plotting functions to represent and inspect the final results of the analysis. The yeast case study demonstrates DChIPRep’s favourable performance when compared to a pipeline inspired by the csaw-package for differential binding analysis.

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DChIPRep classification

DChIPRep specifications

Software type:
Package/Module
Restrictions to use:
None
Input format:
TXT, SAM
Programming languages:
Python, R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Input data:
DChIPRep uses biological replicate information as well as chromatin Input data to allow for a rigorous assessment of differential enrichment.
Operating system:
Unix/Linux, Mac OS, Windows
License:
MIT License
Version:
1.4.0
Requirements:
HTSeq, Numpy, Argparse

DChIPRep distribution

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DChIPRep support

Documentation

Maintainer

  • Bernd Klaus <>

Credits

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Publications

Institution(s)

Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Oncology iMed, CRUK-Cambridge Institute, Astra Zeneca, Cambridge, UK; Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA

Funding source(s)

This work was supported by a PhD fellowship from Boerhinger Ingelheim Fonds; and the Deutsche Forschungsgemeinschaft (1422/3-1).

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