DChIPRep specifications


Unique identifier OMICS_13494
Name DChIPRep
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data DChIPRep uses biological replicate information as well as chromatin Input data to allow for a rigorous assessment of differential enrichment.
Input format TXT, SAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python, R
License MIT License
Computer skills Advanced
Version 1.10.0
Stability Stable
methods, stats, plyr, GenomicRanges, utils, testthat, S4Vectors, BiocStyle, SummarizedExperiment, ggplot2, DESeq2, ChIPpeakAnno, rmarkdown, knitr, reshape2, mgcv, tidyr, fdrtool, R(>=3.4), purrr, smoothmest, assertthat, soGGi
Maintained Yes




No version available



  • person_outline Bernd Klaus

Publication for DChIPRep

DChIPRep citation


A high resolution map of transcriptional repression

PMCID: 5373822
PMID: 28318487
DOI: 10.7554/eLife.22767.036

[…] d to the DEseq2 model as normalisation factors (). MNase signal over Ikaros ChIP-seq peaks () was calculated using the Bioconductor soGGi package () and differential MNase signal identified using the DChIPrep package (). Differential gene expression was based on a p-value of <0.05 after Benjamini-Hochberg correction for multiple testing (adj. p<0.05). To assess the impact of nuclear Ikaros on I […]

DChIPRep 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
DChIPRep 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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