Package: CexoR 1.51.0

Pedro Madrigal

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 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.

Authors:Pedro Madrigal [aut, cre]

CexoR_1.51.0.tar.gz
CexoR_1.51.0.zip(r-4.7)CexoR_1.51.0.zip(r-4.6)CexoR_1.51.0.zip(r-4.5)
CexoR_1.51.0.tgz(r-4.6-any)CexoR_1.51.0.tgz(r-4.5-any)
CexoR_1.51.0.tar.gz(r-4.7-any)CexoR_1.51.0.tar.gz(r-4.6-any)
CexoR_1.51.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
CexoR/json (API)

# Install 'CexoR' in R:
install.packages('CexoR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pmb59/cexor/issues

On BioConductor:CexoR-1.51.0(bioc 3.24)CexoR-1.50.0(bioc 3.23)

functionalgenomicssequencingcoveragechipseqpeakdetectionbioc-devel

4.95 score 6 scripts 457 downloads 1 mentions 4 exports 93 dependencies

Last updated from:9385e58314. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR198
linux-devel-x86_64NOTE430
source / vignettesOK342
linux-release-x86_64NOTE399
macos-release-arm64NOTE302
macos-oldrel-arm64NOTE271
windows-develNOTE360
windows-releaseNOTE343
windows-oldrelNOTE332
wasm-releaseOK158

Exports:cexorplotcexorpskellampskellam.sp

Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsBSgenomecigarilloclicliprcodetoolscpp11crayoncurldata.tableDelayedArrayfarverformatRfutile.loggerfutile.optionsgenericsgenomationGenomicAlignmentsGenomicRangesggplot2gluegridBasegtablehmshttridrimputeIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigplotrixplyrprettyunitsprogressR6RColorBrewerRcppRCurlreadrreshape2restfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfoseqPatternsnowSparseArraystringistringrSummarizedExperimentsystibbletidyselecttzdbutf8vctrsviridisLitevroomwithrXMLXVectoryaml

CexoR Vignette

Rendered fromCexoR.Rnwusingutils::Sweaveon Jun 04 2026.

Last update: 2022-05-28
Started: 2013-11-01