Manual: differential network analysis of gene expression data

This manual provides detailed steps on how to conduct a differential network analysis using the _dnapath_ R package. The manual walks through an application, where we download BAM files from FaceBase, pre-process the counts using TPM normalization and a log transformation, perform the differential network analysis, then summarize and visualize the results. The interpretation of the results is discussed at length, and one approach for validating initial results is shown.