Package: CexoR 1.45.0

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]

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CexoR.pdf |CexoR.html✨
CexoR/json (API)

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

Peer review:

On BioConductor:CexoR-1.45.0(bioc 3.21)CexoR-1.44.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

functionalgenomicssequencingcoveragechipseqpeakdetection

4.00 score 1 scripts 260 downloads 1 mentions 4 exports 98 dependencies

Last updated 3 months agofrom:bc1c514b05. Checks:1 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 28 2025
R-4.5-winNOTEJan 28 2025
R-4.5-linuxNOTEJan 28 2025
R-4.4-winNOTEJan 28 2025
R-4.4-macNOTEJan 28 2025
R-4.3-winNOTEJan 28 2025
R-4.3-macNOTEJan 28 2025

Exports:cexorplotcexorpskellampskellam.sp

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsBSgenomeclicliprcodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayfansifarverformatRfutile.loggerfutile.optionsgenericsgenomationGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegridBasegtablehmshttridrimputeIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplotrixplyrprettyunitsprogressR6RColorBrewerRcppRCurlreadrreshape2restfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalesseqPatternsnowSparseArraystringistringrSummarizedExperimentsystibbletidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLXVectoryaml

CexoR Vignette

Rendered fromCexoR.Rnwusingutils::Sweaveon Jan 28 2025.

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