Package: CexoR
Version: 1.49.0
Date: 2025-07-22
Type: Package
Title: An R package to uncover high-resolution protein-DNA interactions
        in ChIP-exo replicates
Authors@R: 
    c(person(given = "Pedro",
           family = "Madrigal",
           role = c("aut", "cre"),
           email = "pmadrigal@ebi.ac.uk",
           comment = c(ORCID = "0000-0003-1959-8199")
      )
    )
Description: 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.
Depends: R (>= 4.2.0), S4Vectors, IRanges
Imports: Rsamtools, Seqinfo, GenomicRanges, rtracklayer, idr,
        RColorBrewer, genomation
Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
License: Artistic-2.0 | GPL-2 + file LICENSE
biocViews: FunctionalGenomics, Sequencing, Coverage, ChIPSeq,
        PeakDetection
URL: https://github.com/pmb59/CexoR
BugReports: https://github.com/pmb59/CexoR/issues
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libxml2-dev
        libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:12:38 UTC
RemoteUrl: https://github.com/bioc/CexoR
RemoteRef: HEAD
RemoteSha: e9655e9ad95c7c8b5cfecd88ac85647d1b06f658
NeedsCompilation: no
Packaged: 2025-11-12 07:27:12 UTC; root
Author: Pedro Madrigal [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1959-8199>)
Maintainer: Pedro Madrigal <pmadrigal@ebi.ac.uk>
Built: R 4.6.0; ; 2025-11-12 07:32:26 UTC; windows
