Multiscale embedded gene co-expression network analysis
This is a routine MEGENA pipeline description encompassing from data correlation analysis to module plotting, and is based on version 1.3.6 https://CRAN.R-project.org/package=MEGENA. The code was adapted by Giacomo von Alvensleben to fix some issues in the computation of signed correlations and to improve performances in terms of speed. Please cite the paper below when MEGENA is applied as part of your analysis:
Song W.-M., Zhang B. (2015) Multiscale Embedded Gene Co-expression Network Analysis. PLoS Comput Biol 11(11): e1004574. doi: 10.1371/journal.pcbi.1004574.
For statistical mechanics aspects involved in MEGENA, please check:
Song W.-M., Di Matteo T.and Aste T., Building Complex Networks with Platonic Solids, Physical Reivew E, 2012 Apr;85(4 Pt 2):046115.
For installation for developmental github version:
remotes::install_github("vonalven/MEGENA");