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README.md

PhenoGeneRanker

Paper

https://www.biorxiv.org/content/10.1101/651000v1

What is PhenoGeneRanker?

PhenoGeneRanker is a gene/disease prioritization tool that utilizes heterogeneous gene disease network. PhenoGeneRanker allows multi-layer gene and disease networks. It also calculates empirical p-values of gene ranking using random stratified sampling of genes based on their connectivity degree in the network.

GenerateWalkMatrix.R

Generates Complete Multiplex Heterogeneous Network (Walk Matrix - WM) using multiple gene/protein layers and phenotype layers.

RunRWR.R

Takes gene and phenotype seed file as input, and runs the RWR on Complete Multiplex Heterogenous WM and generates ranking results.

PhenoGeneRankerFunctions.R

Functions are used by GenerateWalkMatrix.R and RunRWR.R

Utils.R

Some utility functions.

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