# lncRna <img src="inst/img/lncRna_logo.png" align="right" height = 150/>
## Introduction
**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.
## Core functionality
* **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.
## Example Visualizations
The package allows for easy generation of various plots, such as Venn diagrams for coding potential results:
## Installation
You can install the `lncRna` package using `BiocManager` from Bioconductor:
```r
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("lncRna")
```
or directly from Github
```r
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("prodakt/lncRna")
```
## Getting Started
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:
```r
library(lncRna)
vignette("lncRna")
