CexoR: An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
Version 1.14.0

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 for overlapping peak-pairs across biological replicates is estimated using the package 'idr'.

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AuthorPedro Madrigal <pm12@sanger.ac.uk>
Bioconductor views Genetics Sequencing Transcription
Date of publicationNone
MaintainerPedro Madrigal <pm12@sanger.ac.uk>
LicenseArtistic-2.0 | GPL-2 + file LICENSE
Version1.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CexoR")

Man pages

cexor: ChIP-exo peak-pair calling with replicates
CexoR-internal: CexoR internal functions
CexoR-package: An R package to uncover high-resolution protein-DNA...
plotcexor: Visualization of ChIP-exo peak-pair calling with replicates

Functions

CexoR Man page
CexoR-package Man page
cexor Man page Source code
plotcexor Man page Source code
pskellam Man page Source code
pskellam.sp Man page Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/cexor.R
R/plotcexor.R
R/pskellam.R
R/pskellam.sp.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/CexoR.R
inst/doc/CexoR.Rnw
inst/doc/CexoR.pdf
inst/extdata
inst/extdata/CTCF_rep1_chr2_1-1e6.bam
inst/extdata/CTCF_rep1_chr2_1-1e6.bam.bai
inst/extdata/CTCF_rep2_chr2_1-1e6.bam
inst/extdata/CTCF_rep2_chr2_1-1e6.bam.bai
inst/extdata/CTCF_rep3_chr2_1-1e6.bam
inst/extdata/CTCF_rep3_chr2_1-1e6.bam.bai
inst/unitTests
inst/unitTests/test_cexor.R
man
man/CexoR-internal.Rd
man/CexoR-package.Rd
man/cexor.Rd
man/plotcexor.Rd
tests
tests/runTests.R
vignettes
vignettes/CexoR.Rnw
CexoR documentation built on May 20, 2017, 9:16 p.m.