Package: MEGENA 1.6

MEGENA: Multiscale Clustering of Geometrical Network

Co-Expression Network Analysis by adopting network embedding technique. 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>.

Authors:Won-Min Song, Bin Zhang

MEGENA_1.6.tar.gz
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MEGENA.pdf |MEGENA.html✨
MEGENA/json (API)

# Install 'MEGENA' in R:

install.packages('MEGENA', repos = c('https://songw01.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/songw01/megena/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

datExpr - Toy example data

On CRAN:

19 exports 48 stars 4.46 score 73 dependencies 1 dependents 23 mentions 42 scripts 232 downloads

Last updated 8 months agofrom:8f4f98e4d4. Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 05 2024
R-4.5-win-x86_64	WARNING	Sep 05 2024
R-4.5-linux-x86_64	WARNING	Sep 05 2024
R-4.4-win-x86_64	WARNING	Sep 05 2024
R-4.4-mac-x86_64	WARNING	Sep 05 2024
R-4.4-mac-aarch64	WARNING	Sep 05 2024
R-4.3-win-x86_64	WARNING	Sep 05 2024
R-4.3-mac-x86_64	WARNING	Sep 05 2024
R-4.3-mac-aarch64	WARNING	Sep 05 2024

Exports:calculate.PFN calculate.rho.signed compute.PFN.par do.MEGENA draw_sunburst_wt_fill get_module_hierarchy_graph get.DegreeHubStatistic get.hub.summary get.union.cut MEGENA.ModuleSummary module_convert_to_table output.geneSet.file perform.AllPairs.FET perform.ijPairs.FET planaritytest plot_module plot_module_hierarchy plot_subgraph read.geneSet

Dependencies:BH cachem class cli cluster codetools colorspace cpp11 DEoptimR diptest doParallel dplyr fansi farver fastmap flexmix foreach fpc generics ggforce ggplot2 ggraph ggrepel glue graphlayouts gridExtra gtable igraph impute isoband iterators kernlab labeling lattice lifecycle magrittr MASS Matrix mclust memoise mgcv modeltools munsell nlme nnet pillar pkgconfig plyr polyclip prabclus purrr R6 RColorBrewer Rcpp RcppArmadillo RcppEigen reshape rlang robustbase scales stringi stringr systemfonts tibble tidygraph tidyr tidyselect tweenr utf8 vctrs viridis viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
co-expression network analysis	MEGENA-package MEGENA
PFN calculation	calculate.PFN resume.calculate.PFN
correlation calculation	calculate.rho.signed
Parallelized PFN computation	compute.PFN.par
Toy example data	datExpr
MEGENA clustering + MHA	do.MEGENA
Draw sunburst plot showing MEGENA module hierarchy.	draw_sunburst_wt_fill
Curated MSigDB signatures for testing funtion/pathway enrichments of MEGENA modules	FrequenctSets.v6.2.RData
Module Hierarchy Visualization	get_module_hierarchy_graph
calculate module degree statistics based on random triangulation model via T1 and T2 moves.	get.DegreeHubStatistic
summarize hub information.	get.hub.summary
Scale-thresholding of multiscale modules.	get.union.cut
MEGENA module summary	MEGENA.ModuleSummary
conversion of module list object to a data.frame table format	module_convert_to_table
output gene signatures into .gmt file format	output.geneSet.file
Fisher Exact Test (FET) analysis for ALL possible pairs of two gene set lists.	perform.AllPairs.FET
Fisher Exact Test (FET) analysis for user specific pairs of gene sets	perform.ijPairs.FET
Boyer-Myvold Planarity test of a network	planaritytest
Module plotting function.	plot_module
Plot module hierarchy	plot_module_hierarchy
subnetwork plotting functionality.	plot_subgraph
.gmt file reader function	read.geneSet
Toy example data	Sample_Expression.RData