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EvORanker

EvORanker is a software that implements phylogenetic profiling and STRING-based prioritization of candidate genes for human diseases.

Introduction

EvORanker is the first platform that leverages a clade-wise phylogenetic profiling (PP) approach to associate gene variants in patients with their phenotypes. It is particularly useful for identifying disease associations for genes that may not have been previously characterized or published.

Releases

EvORanker is also available as a web server at here.

Dependencies

  • R (version 3.6 or higher)

Installation

Please clone the repository into your computer:

git clone https://github.com/ccanavati/EvoRanker

Then enter the EvoRanker directory:

cd EvoRanker

Synopsis

  • Indirectly prioritize genes based on PP and STRING (The smaller the p-value, the stronger the evidence against the null hypothesis, indicating a more significant association for the gene):
Rscript PP_STRING_gene_prioritization.R example_genes.txt HP:0001250 HP:0002392 output_file.csv
  • Directly prioritize genes based on association with the phenotype(s) (without PP and STRING) using OntologySimilarity tool*
Rscript Direct_gene_prioritization.R example_genes.txt HP:0001250 HP:0002392 output_file.csv

*Greene D, Richardson S, Turro E. ontologyX: a suite of R packages for working with ontological data. Bioinformatics. 2017 Apr 1;33(7):1104–6.

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