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MEGENA

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.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.

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Version

Install

install.packages('MEGENA')

Monthly Downloads

207

Version

1.3.7

License

GPL (>= 3)

Issues

16

Pull Requests

1

Stars

48

Forks

16

Maintainer

WonMin Song

Last Published

September 10th, 2018

Functions in MEGENA (1.3.7)

datExpr

Toy example data
plot_module

Module plotting function.
Sample_Expression

Toy example data
calculate.PFN

PFN calculation
read.geneSet

.gmt file reader function
module_convert_to_table

conversion of module list object to a data.frame table format
output.geneSet.file

output gene signatures into .gmt file format
draw_sunburst_wt_fill

Draw sunburst plot showing MEGENA module hierarchy.
get.DegreeHubStatistic

calculate module degree statistics based on random triangulation model via T1 and T2 moves.
MEGENA-package

co-expression network analysis
MEGENA.ModuleSummary

MEGENA module summary
plot_module_hierarchy

Plot module hierarchy
plot_subgraph

subnetwork plotting functionality.
get.hub.summary

summarize hub information.
calculate.correlation

correlation calculation
compute.PFN.par

Parallelized PFN computation
get.union.cut

Scale-thresholding of multiscale modules.
do.MEGENA

MEGENA clustering + MHA
planaritytest

Boyer-Myvold Planarity test of a network