Package: DuplexDiscovereR
Title: Analysis of the data from RNA duplex probing experiments
Authors@R: 
        c(person("Egor", "Semenchenko", , 
        email = "yegor.smb@gmail.com", 
        role = c("aut", "cre","cph"),
        comment = c(ORCID = "0009-0007-5306-076X")),
        person("Volodymyr", "Tsybulskyi", ,
        email = "Volodymyr.Tsybulskyi@mdc-berlin.de", role = c("ctb"),
        comment = c(ORCID = "0009-0002-4141-6291")),
        person("Irmtraud M.", "Meyer", ,
        email = "irmtraud.m.meyer@cantab.net", role = c("aut","cph"),
             comment = c(ORCID = "0000-0002-4048-3479")))
Description: 
   DuplexDiscovereR is a package designed for analyzing data from RNA 
   cross-linking and proximity ligation protocols such as SPLASH, PARIS, 
   LIGR-seq, and others.
   DuplexDiscovereR accepts input in the form of chimerically or
   split-aligned reads. It includes procedures for alignment classification,
   filtering, and efficient clustering of individual chimeric reads into duplex 
   groups (DGs). Once DGs are identified, the package predicts RNA duplex 
   formation and their hybridization energies. Additional metrics, such as
   p-values for random ligation hypothesis or mean DG alignment scores, 
   can be calculated to rank final set of RNA duplexes.
   Data from multiple experiments or replicates can be processed separately 
   and further compared to check the reproducibility of the experimental method.
License: GPL-3
URL: https://github.com/Egors01/DuplexDiscovereR/
BugReports: https://github.com/Egors01/DuplexDiscovereR/issues/
Encoding: UTF-8
NeedsCompilation: no
Version: 1.3.1
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
BiocType: Software
biocViews: Sequencing, Transcriptomics, StructuralPrediction,
        Clustering, SplicedAlignment
Imports: Gviz, Biostrings, rtracklayer, GenomicAlignments,
        GenomicRanges, ggsci, igraph, rlang, scales, stringr, dplyr,
        tibble, tidyr, purrr, methods, grDevices, stats, utils
Depends: R (>= 4.4), InteractionSet
LazyData: false
Suggests: knitr, UpSetR, BiocStyle, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
VignetteEngine: knitr
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/DuplexDiscovereR
git_branch: devel
git_last_commit: 16328fb
git_last_commit_date: 2025-07-11
Repository: Bioconductor 3.22
Date/Publication: 2025-07-11
Packaged: 2025-07-11 22:43:00 UTC; biocbuild
Author: Egor Semenchenko [aut, cre, cph] (ORCID:
    <https://orcid.org/0009-0007-5306-076X>),
  Volodymyr Tsybulskyi [ctb] (ORCID:
    <https://orcid.org/0009-0002-4141-6291>),
  Irmtraud M. Meyer [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-4048-3479>)
Maintainer: Egor Semenchenko <yegor.smb@gmail.com>
Built: R 4.5.1; ; 2025-07-12 12:46:19 UTC; windows
