HAN-Siyu / LION

An Integrated R Package for Effective Prediction of ncRNA- and lncRNA-protein Interaction
https://doi.org/10.1093/bib/bbac420
GNU General Public License v3.0
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LION

An integrated R package for effective prediction of lncRNA- and ncRNA-protein interaction

Understanding ncRNA-protein interaction is of critical importance to unveil ncRNAs' functions. Now many computational tools have been developed to facilitate the research on ncRNA-protein interaction. Nonetheless, the majority of these tools show unstable results and lack the flexibility required by dataset-specific prediction. Here we propose an integrated package LION which comprises a new method for predicting ncRNA/lncRNA-protein interaction as well as a comprehensive strategy to meet the requirement of customisable prediction. As an integrated tool for predicting ncRNA-protein interaction, LION can be used to build adaptable models for species and tissue-specific prediction and considerably enhance the performance of several widely-used tools. Experimental results also demonstrate our method outperforms its competitors on multiple benchmark datasets. We expect LION will be a powerful and efficient tool for the prediction and analysis of ncRNA- and lncRNA-protein interaction.

Thank you for checking our LION @BigCatZoo!

Any questions regarding LION please drop an email to the zookeeper Siyu Han (siyu.han@tum.de) or post it to issues.

Install LION

Using devtools

# Enter the following command in R:

if (!library("devtools", logical.return = T)) install.packages("devtools")
devtools::install_github("HAN-Siyu/LION")

Or Download Source Package Here and Install Manually.

Versions below v0.2.9.1 has a issue in calculating metrics. The issue did not affect the results reported in our paper. We recommend using the latest version. Update details can be found in NEWS.

Habitat

Almost all dependencies will be installed when installing LION in R. However, secondary strucutre features are computed using standalone software, RNAsubopt (from ViennaRNA package) and Predator. You need to download these two programmes if you would like to use method lncPro or extract structural features.

Supporting Files

[PDF Manual] [Datasets and Raw Results]

How to Train Your LION

We expect LION could be a powerful package for predicting RNA-protein interaction in a uniform R environment. The functions of LION can be categorized into several groups to facilitate feature extraction, interaction prediction and model tuning. We here provide a basic summary for LION's function. Detailed examples and parameters explanations can be found in our manual.

Functions for feature extraction

Functions for feature set construction

Functions for random forestion model training

Functions for RNA-protein prediction with different methods

Other Utilities

Cite This Work

To cite LION in publications, please use:

Siyu Han, Xiao Yang, Hang Sun, Yang Hu, Qi Zhang, Cheng Peng, Wensi Fang, Ying Li. LION: an integrated R package for effective prediction of ncRNA–protein interaction. Briefings in bioinformatics. 2022; 23(6):bbac420. (doi: https://doi.org/10.1093/bib/bbac420)

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