DOI: 10.18129/B9.bioc.CexoR    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see CexoR.

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

Bioconductor version: 3.13

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function (package 'skellam') is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Irreproducible discovery rate (IDR) for overlapping peak-pairs across biological replicates is estimated using the package 'idr'.

Author: Pedro Madrigal <bioinformatics.engineer at gmail.com>

Maintainer: Pedro Madrigal <pmadrigal at ebi.ac.uk>

Citation (from within R, enter citation("CexoR")):


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biocViews Genetics, Sequencing, Software, Transcription
Version 1.30.1
In Bioconductor since BioC 2.13 (R-3.0) (8 years)
License Artistic-2.0 | GPL-2 + file LICENSE
Depends R (>= 2.10.0), S4Vectors, IRanges
Imports Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation
Suggests RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
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