CoGA: An R Package to Identify Differentially Co-Expressed Gene Sets by Analyzing the Graph Spectra
Fig 1
CoGA Overview: (A) input data, (B) CoGA differential network analysis, and (C) CoGA further analysis.
The CoGA package receives as input data a gene expression matrix, the sample labels, and a collection of gene sets. Then, it constructs a gene co-expression sub-graph for each gene set, and tests the equality in the network structural features between two biological conditions (B). The software allows the user to further analyze each gene set (C) by visualizing the gene co-expression graphs, ranking the genes according to their “importance” in the gene set network, and performing standard single gene differential expression analysis.