Package: lncRna
Title: A Comprehensive Workflow for Long Non-coding RNA Identification
        and Functional Analysis
Version: 1.1.0
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
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libssl-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:07:14 UTC
RemoteUrl: https://github.com/bioc/lncRna
RemoteRef: HEAD
RemoteSha: ae94230cbb791cb2e13b18e9e8555f7a054f1ebc
NeedsCompilation: no
Packaged: 2026-06-05 06:31:43 UTC; root
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>