lncRna
This is the development version of lncRna; for the stable release version, see lncRna.
All Bioconductor versions of lncRna
3.24 (devel), 3.23 (release)
A Comprehensive Workflow for Long Non-coding RNA Identification and Functional Analysis
Bioconductor version: 3.24 · Package version: 1.1.0
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.
Author: Jan Pawel Jastrzebski [aut, cre] 
, Damian Czopek [ctb, aut] , Mariusz Jankowski [ctb] , Monika Gawronska [ctb] , Wiktor Babis [ctb] , Stefano Pascarella [ctb] , Hugo Gruson [ctb]
Maintainer: Jan Pawel Jastrzebski <bioinformatyka at gmail.com>
Citation
From within R, enter citation("lncRna"):
Jan Pawel Jastrzebski, Damian Czopek. lncRna: A Comprehensive Workflow for Long Non-coding RNA Identification and Functional Analysis. doi:10.18129/B9.bioc.lncRna, R package version 1.1.0, https://bioconductor.org/packages/lncRna.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("lncRna")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.1.0 |
| License | MIT + file LICENSE |
| URL | https://github.com/prodakt/lncRna |
| Bug Reports | https://github.com/prodakt/lncRna/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.23 (R-4.6) (less than a year) |
| Downloads rank | 2314 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, FunctionalGenomics, FunctionalPrediction, GeneExpression, QualityControl, RNASeq, Software, Transcription, Visualization |
| Package Short Url | https://bioconductor.org/packages/lncRna/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("lncRna")| lncRna: A Comprehensive Pipeline for lncRNA Identification and Functional Analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | lncRna_1.1.0.tar.gz |
| Windows binary (x86_64) | lncRna_1.1.0.zip |
| macOS binary (arm64) | lncRna_1.1.0.tgz |
| macOS binary (x86_64) | lncRna_1.1.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/lncRna |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/lncRna |
| Package Downloads Report | Download Stats |
Dependencies
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