Package: lncRna
Title: A Comprehensive Workflow for Long Non-coding RNA Identification
        and Functional Analysis
Version: 0.99.3
Authors@R: c(
    person(given = "Jan Pawel",
           family = "Jastrzebski",
           role = c("aut", "cre"),
           email = "bioinformatyka@gmail.com",
           comment = c(ORCID = "0000-0001-8699-7742")),
    person(given = "Damian",
           family = "Czopek",        
           role = c("ctb", "aut"),          
           email = "dcwmpl@gmail.com",
           comment = c(ORCID = "0009-0005-3471-4866")),
	person(given = "Mariusz",
           family = "Jankowski",        
           role = c("ctb"),          
           email = "ma.jankowski99@gmail.com",
           comment = c(ORCID = "0009-0000-7872-4023")),
    person(given = "Monika",
           family = "Gawronska",    
           role = c("ctb"),
           email = "gawronska572@gmail.com",
           comment = c(ORCID = "0009-0001-2677-6371")), 
    person(given = "Wiktor",
           family = "Babis",        
           role = c("ctb"),          
           email = "wiktorbabis@gmail.com",
           comment = c(ORCID = "0009-0006-3648-3413")),
    person(given = "Stefano",
           family = "Pascarella",        
           role = c("ctb"),          
           email = "stefano.pascarella@uniroma1.it",
           comment = c(ORCID = "0000-0002-6822-4022")),
	person("Hugo", "Gruson", , 
			"hugo.gruson+R@normalesup.org", 
			role = c("ctb"),
           comment = c(ORCID = "0000-0002-4094-1476"))
	)
Description: Provides a complete workflow for the identification, analysis, and functional
    annotation of long non-coding RNAs (lncRNAs) from RNA-Seq data. The package
    includes functions for filtering transcripts from GTF files, evaluating the
    performance of multiple coding potential prediction tools (e.g., CPC2, PLEK,
    CPAT), and summarizing their agreement. It enables systematic performance
    analysis of individual tools, "at least N" tool consensus, and all possible tool
    combinations. Functional analysis is supported through the identification of
    potential cis- and trans-acting interactions with protein-coding genes,
    followed by enrichment analysis. Results can be visualized using a variety
    of plots, including radar plots, clock plots, and interactive Sankey diagrams.
License: MIT + file LICENSE
URL: https://github.com/prodakt/lncRna
BugReports: https://github.com/prodakt/lncRna/issues
biocViews: Software, GeneExpression, RNASeq, Transcription,
        Visualization, QualityControl, FunctionalGenomics,
        Classification, FunctionalPrediction
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Imports: fmsb, ggplot2, grDevices, graphics, Hmisc, patchwork, plotly,
        Polychrome, tidyr, S4Vectors, scales, stats, stringr,
        GenomicRanges, utils
Suggests: IRanges, methods, BiocStyle, gprofiler2, knitr, rmarkdown,
        rtracklayer, seqinr, testthat (>= 3.0.0), venn
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/lncRna
git_branch: devel
git_last_commit: cc94632
git_last_commit_date: 2026-03-11
Repository: Bioconductor 3.23
Date/Publication: 2026-04-24
NeedsCompilation: no
Packaged: 2026-04-24 22:33:56 UTC; biocbuild
Author: Jan Pawel Jastrzebski [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8699-7742>),
  Damian Czopek [ctb, aut] (ORCID:
    <https://orcid.org/0009-0005-3471-4866>),
  Mariusz Jankowski [ctb] (ORCID:
    <https://orcid.org/0009-0000-7872-4023>),
  Monika Gawronska [ctb] (ORCID: <https://orcid.org/0009-0001-2677-6371>),
  Wiktor Babis [ctb] (ORCID: <https://orcid.org/0009-0006-3648-3413>),
  Stefano Pascarella [ctb] (ORCID:
    <https://orcid.org/0000-0002-6822-4022>),
  Hugo Gruson [ctb] (ORCID: <https://orcid.org/0000-0002-4094-1476>)
Maintainer: Jan Pawel Jastrzebski <bioinformatyka@gmail.com>
