lncRna is an R package designed to simplify and streamline the process of long non-coding RNA (lncRNA) identification and functional analysis.
Accurate identification and functional annotation of lncRNAs are critical for understanding their regulatory roles in complex biological processes. This package provides a comprehensive, user-friendly interface for processing transcriptomic data, implementing lncRNA identification pipelines, and systematically evaluating the performance of multiple coding-potential prediction tools.
Easy Pipeline Setup: Filter transcripts from GTF files based on structural features and expression levels.
Coding Potential Assessment: Integrate and evaluate results from multiple external prediction tools (e.g., CPC2, PLEK, CPAT).
Statistical Evaluation: Compute key metrics (accuracy, precision, sensitivity) to select the most reliable lncRNA identification strategy (including tool combinations and "at least N" consensus).
Functional Annotation: Identify potential cis- and trans-acting interactions with protein-coding genes and perform functional enrichment analysis.
Visualization: Generate informative plots (radar plots, clock plots, interactive Sankey diagrams, Venn diagrams) to visualize performance and interaction results.
The package allows for easy generation of various plots, such as Venn diagrams for coding potential results:
You can install the lncRna package using BiocManager from Bioconductor:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("lncRna")
or directly from Github
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("prodakt/lncRna")
To get started with lncRna, please read the package vignette which contains a complete, step-by-step tutorial on how to use the package functions:
library(lncRna)
vignette("lncRna")