Last Update: 17 March 2024 染山

参考脚本:

WGCNA Gene Correlation Network Analysis

https://mp.weixin.qq.com/s/5OUY5KDwgi05MlFrV_7Qjw

Network analysis with WGCNA

WGCNA R 包根据表达数据构建“加权基因共表达网络分析”。最初发表于 2008 年，引用如下：

• Langfelder, P. and Horvath, S., 2008. WGCNA: an R package for weighted correlation network analysis. BMC bioinformatics, 9(1), p.559.
• Zhang, B. and Horvath, S., 2005. A general framework for weighted gene co-expression network analysis. Statistical applications in genetics and molecular biology, 4(1).

更多信息

• Recent PubMed Papers
• Original WGCNA tutorials - Last updated 2016
• Video: ISCB Workshop 2016 - Co-expression network analysis using RNA-Seq data (Keith Hughitt)

Installing WGCNA

install.packages(c("tidyverse", "magrittr", "WGCNA"))

Overview

The WGCNA pipeline is expecting an input matrix of RNA Sequence counts. Usually we need to rotate (transpose) the input data so rows = treatments and columns = gene probes.