DOI: 10.18129/B9.bioc.CexoR    

This is the development version of CexoR; for the stable release version, see CexoR.

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

Bioconductor version: Development (3.17)

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Then, irreproducible discovery rate for overlapping peak-pairs across biological replicates is computed.

Author: Pedro Madrigal [aut, cre]

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

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PDF R Script CexoR Vignette
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biocViews ChIPSeq, Coverage, FunctionalGenomics, PeakDetection, Sequencing, Software
Version 1.37.0
In Bioconductor since BioC 2.13 (R-3.0) (9 years)
License Artistic-2.0 | GPL-2 + file LICENSE
Depends R (>= 4.2.0), S4Vectors, IRanges
Imports Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation
Suggests RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
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Source Package CexoR_1.37.0.tar.gz
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