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

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'.

Author
Pedro Madrigal <pm12@sanger.ac.uk>
Date of publication
None
Maintainer
Pedro Madrigal <pm12@sanger.ac.uk>
License
Artistic-2.0 | GPL-2 + file LICENSE
Version
1.12.0

View on Bioconductor

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

Files in this package

CexoR/DESCRIPTION
CexoR/LICENSE
CexoR/NAMESPACE
CexoR/R
CexoR/R/cexor.R
CexoR/R/plotcexor.R
CexoR/R/pskellam.R
CexoR/R/pskellam.sp.R
CexoR/build
CexoR/build/vignette.rds
CexoR/inst
CexoR/inst/CITATION
CexoR/inst/doc
CexoR/inst/doc/CexoR.R
CexoR/inst/doc/CexoR.Rnw
CexoR/inst/doc/CexoR.pdf
CexoR/inst/extdata
CexoR/inst/extdata/CTCF_rep1_chr2_1-1e6.bam
CexoR/inst/extdata/CTCF_rep1_chr2_1-1e6.bam.bai
CexoR/inst/extdata/CTCF_rep2_chr2_1-1e6.bam
CexoR/inst/extdata/CTCF_rep2_chr2_1-1e6.bam.bai
CexoR/inst/extdata/CTCF_rep3_chr2_1-1e6.bam
CexoR/inst/extdata/CTCF_rep3_chr2_1-1e6.bam.bai
CexoR/inst/unitTests
CexoR/inst/unitTests/test_cexor.R
CexoR/man
CexoR/man/CexoR-internal.Rd
CexoR/man/CexoR-package.Rd
CexoR/man/cexor.Rd
CexoR/man/plotcexor.Rd
CexoR/tests
CexoR/tests/runTests.R
CexoR/vignettes
CexoR/vignettes/CexoR.Rnw