NetFunrankR: An R package for robust functional enrichment test using Network medicine approach and beyond

With the given biomarker sets, this package primarily facilitates the following analysis:
1. Topology-aware enrichment: Network-proximity based functional enrichment test utilizing protein-protein interaction network
2. Over-representation enrichment Typical hypergeometric-distribution based over-representation test
Results include two spreadsheets, one for ORA-based test, and another for TW-based test. Visualization includes, a venn diagram, double-bar plots and two lollipop plots. This document shows the basic usage of this package.

本工具包基于给定的生物标志物集，主要可实现以下分析功能：
1. 拓扑感知富集分析（Topology-aware enrichment）：利用蛋白质-蛋白质相互作用（protein-protein interaction, PPI）网络的网络邻近性功能富集检验
2. 过度表达富集分析（Over-representation enrichment）：基于超几何分布的经典过度表达检验
分析结果包含两份电子表格，分别对应基于ORA（Over-representation Analysis）的检验结果与基于TW的检验结果。可视化产出涵盖韦恩图（venn diagram）、双条形图（double-bar plots）以及两幅棒棒糖图（lollipop plots）。本文档将介绍本工具包的基础使用方法。