lncRna

This is the development version of lncRna; to use it, please install the devel version of Bioconductor.

A Comprehensive Workflow for Long Non-coding RNA Identification and Functional Analysis

Bioconductor version: Development (3.23)

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] ORCID: 0000-0001-8699-7742 , Damian Czopek [ctb, aut] ORCID: 0009-0005-3471-4866 , Mariusz Jankowski [ctb] ORCID: 0009-0000-7872-4023 , Monika Gawronska [ctb] ORCID: 0009-0001-2677-6371 , Wiktor Babis [ctb] ORCID: 0009-0006-3648-3413 , Stefano Pascarella [ctb] ORCID: 0000-0002-6822-4022 , Hugo Gruson [ctb] ORCID: 0000-0002-4094-1476

Maintainer: Jan Pawel Jastrzebski <bioinformatyka at gmail.com>

Citation (from within R, enter citation("lncRna")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("lncRna")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("lncRna")

lncRna: Identification and Functional Analysis Pipeline	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, FunctionalGenomics, FunctionalPrediction, GeneExpression, QualityControl, RNASeq, Software, Transcription, Visualization
Version	0.99.3
In Bioconductor since	BioC 3.23 (R-4.6)
License	MIT + file LICENSE
Depends
Imports	fmsb, ggplot2, grDevices, graphics, Hmisc, patchwork, plotly, Polychrome, tidyr, S4Vectors, scales, stats, stringr, GenomicRanges, utils
System Requirements
URL	https://github.com/prodakt/lncRna
Bug Reports	https://github.com/prodakt/lncRna/issues

Suggests	IRanges, methods, BiocStyle, gprofiler2, knitr, rmarkdown, rtracklayer, seqinr, testthat (>= 3.0.0), venn
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	lncRna_0.99.3.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (big-sur-arm64)
macOS Binary (sonoma-arm64)	lncRna_0.99.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/lncRna
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/lncRna
Bioc Package Browser	https://code.bioconductor.org/browse/lncRna/
Package Short Url	https://bioconductor.org/packages/lncRna/
Package Downloads Report	Download Stats