NeuroVar: A Genetic Expression and Variation data visualization tool for Neurological diseases’ biomarkers

Table of Contents

1. Background
2. About NeuroVar
3. Demonstration Video
4. Usage Guidelines
5. Code availability
6. License
7. Citation
8. Contributors

Background

The expanding availability of large-scale genomic data and the growing interest in uncovering gene-disease associations call for efficient tools to visualize and evaluate gene expression and genetic variation data.

About NeuroVar

NeuroVar is a novel tool for visualizing genetic variation (Single nucleotide polymorphisms and insertions/deletions) and gene expression data related to neurological diseases. The tool is available as a desktop application that does not require any computational skills to use.

The current version includes :

• 11 Neurological Syndromes are integrated, including:

          ★ Epilepsy
          ★ Amyotrophic lateral sclerosis
          ★ Intellectual disability and Autism spectrum disorder
          ★ Brain malformation syndrome
          ★ Syndromic Disorders
          ★ Cerebral Palsy
          ★ RASopathy
          ★ Aminoacidopathy
          ★ CranioFacial Malformations
          ★ Parkinson disease
          ★ PHARC syndrome
  

• and 7 Non-Neurological diseases with neurological manifestations are integrated, including:

          ★ Peroxisomal disorders  
          ★ Hereditary cancer
          ★ Mitochondrial disease
          ★ Retina-related disorders
          ★ General Gene Curation
          ★ Hearing Loss
          ★ Fatty Acid Oxidation Disorders
  

Demonstration Video

Usage Guidelines

NeuroVar is available as a Shiny Application and a desktop application.

1. Shiny application

Guide : Click Here

2. Desktop application

Guide : Click Here

Demonstration Data

Demonstration data are provided here

This data will guide you to organize your data correctly and could be used to test the tool.

Code availability

The code if the two versions are available open source.

1. Shiny application

Source Code : Click Here

2. Desktop application

Source Code : Click Here

The tool is also registered at SciCrunch.org.

RRID: SCR_025640

License

License : Artistic license 2.0

Citation

Hiba Ben Aribi, Najla Abassi and Olaitan I. Awe. NeuroVar: A Genetic Expression and Variation data visualization tool for Neurological diseases’ biomarkers. Zenodo. https://doi.org/10.5281/zenodo.13375646. RRID: SCR_025640.

Reporting Issues

To report an issue please use the issues page (https://github.com/omicscodeathon/neurovar/issues). Please check existing issues before submitting a new one.

Contribute to Project

You can offer to help with the further development of this project by making pull requests on this repo. To do so, fork this repository and make the proposed changes. Once completed and tested, submit a pull request to this repo.

Contributors

Hiba Ben Aribi, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia (Developer - Writer).

Najla Abassi, Pasteur Institute of Tunis, Tunisia (Developer - Writer).

Olaitan I. Awe, African Society for Bioinformatics and Computational Biology (ASBCB), Cape Town, South Africa.