fRNC-package: fRNC: Search for modules in a node-weighted ncRNA network

In leiming8886/fRNC: ncRNA module search functions

fRNC: Search for modules in a node-weighted ncRNA network

Description

fRNC constructs a node-weighted ncRNA network, performs module searching, generates simulation data from random networks, normalizes module scores using simulation data, removes un-qualified modules, and orders resultant modules according to their significance.

Details

This package takes three types of data as input: a list of genes with association p-values and logFC, a human ncRNA network. generate_graph constructs a node-weighted ncRNA network. runmodule performs module search upon the node-weighted ncRNA network.

References

Hongbo Shi, Jiayao Li, Qiong Song et al. (2019) Systematic identification and analysis of dysregulated miRNA and transcription factor feed-forward loops in hypertrophic cardiomyopathy

Peilin Jia, Siyuan Zheng, Jirong Rong, Wei Zheng, Zhongming Zhao. (2011) Bioformatics. dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks.

leiming8886/fRNC documentation built on Feb. 21, 2023, 4:12 p.m.