DuplexDiscovereR

[Egors01]

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[bioc-issue-bot]

Hi @Egors01

Thanks for submitting your package. We are taking a quick
look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: DuplexDiscovereR
Title: Analysis of the data from RNA duplex probing experiments
Authors@R: 
        c(person("Egor", "Semenchenko", , 
        email = "[email protected]", 
        role = c("aut", "cre","cph"),
        comment = c(ORCID = "0009-0007-5306-076X")),
        person("Volodymyr", "Tsybulskyi", ,
        email = "[email protected]", role = c("ctb"),
        comment = c(ORCID = "0009-0002-4141-6291")),
        person("Irmtraud M.", "Meyer", ,
        email = "[email protected]", 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/Duplex_Explorer
BugReports: https://github.com/Egors01/Duplex_Explorer
Encoding: UTF-8
NeedsCompilation: no
Version: 0.99.0
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
BiocType: Software
biocViews: 
  Sequencing,
  Transcriptomics,
  StructuralPrediction,
  Clustering,
  SplicedAlignment
Imports: 
    Gviz,
    Biostrings,
    rtracklayer,
    digest,
    GenomicAlignments,
    dplyr,
    ggsci,
    igraph,
    rlang,
    scales,
    stringr,
    tibble,
    tidyr,
    purrr,
    methods
Depends: 
    R (>= 4.4),
    InteractionSet
LazyData: false
Suggests: 
    knitr,
    UpSetR,
    BiocStyle,
    rmarkdown,
    testthat (>= 3.0.0)
VignetteBuilder: knitr
VignetteEngine: knitr
Config/testthat/edition: 3

[bioc-issue-bot]

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[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): DuplexDiscovereR_0.99.0.tar.gz
macOS 12.7.1 Monterey: DuplexDiscovereR_0.99.0.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/DuplexDiscovereR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.