lncRna
A Comprehensive Workflow for Long Non-coding RNA Identification and Functional Analysis
Bioconductor version: 3.23 · Package version: 1.0.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("lncRna")Details
| Maintainer | Jan Pawel Jastrzebski <bioinformatyka@gmail.com> |
| 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>) |
| License | MIT + file LICENSE |
| URL | https://github.com/prodakt/lncRna |
| Bug Reports | https://github.com/prodakt/lncRna/issues |
| Source branch | RELEASE_3_23 |
| 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/ |
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 1.0.0, https://bioconductor.org/packages/lncRna.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | lncRna_1.0.0.tar.gz |
| Windows binary (x86_64) | lncRna_1.0.0.zip |
| macOS binary (arm64) | lncRna_1.0.0.tgz |
| macOS binary (x86_64) | lncRna_1.0.0.tgz |
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