MEGENA: Multiscale Clustering of Geometrical Network

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Co-Expression Network Analysis by adopting network embedding technique.

Author
Won-Min Song, Bin Zhang
Date of publication
2016-10-25 20:31:59
Maintainer
Won-Min Song <wonmin1984@gmail.com>
License
GPL (>= 2)
Version
1.3.5-2

View on CRAN

Man pages

calculate.correlation
correlation calculation
calculate.PFN
PFN calculation
compute.PFN.par
Parallelized PFN computation
datExpr
Toy example data
do.MEGENA
MEGENA clustering + MHA
get.DegreeHubStatistic
calculate module degree statistics based on random...
get.hub.summary
summarize hub information.
get.union.cut
Scale-thresholding of multiscale modules.
MEGENA.ModuleSummary
MEGENA module summary
MEGENA-package
co-expression network analysis
output.geneSet.file
output gene signatures into .gmt file format
planaritytest
Boyer-Myvold Planarity test of a network
plot_module
Module plotting function.
plot_module_hierarchy
Plot module hierarchy
plot_subgraph
subnetwork plotting functionality.
read.geneSet
.gmt file reader function
Sample_Expression
Toy example data

Files in this package

MEGENA
MEGENA/inst
MEGENA/inst/doc
MEGENA/inst/doc/MEGENA_pipeline_10062016.Rmd
MEGENA/inst/doc/MEGENA_pipeline_10062016.html
MEGENA/inst/doc/MEGENA_pipeline_10062016.R
MEGENA/src
MEGENA/src/planaritytest.cpp
MEGENA/src/RcppExports.cpp
MEGENA/NAMESPACE
MEGENA/data
MEGENA/data/Sample_Expression.RData
MEGENA/data/datalist
MEGENA/R
MEGENA/R/CorrelationScreen.R
MEGENA/R/PFN_Computation.R
MEGENA/R/Combined_functions.R
MEGENA/R/ModuleHierarchyPlot.R
MEGENA/R/RcppExports.R
MEGENA/R/ClusteringPackage.R
MEGENA/R/Downstream_TableManip.R
MEGENA/R/NetworkSummary.R
MEGENA/R/ModulePlot.R
MEGENA/vignettes
MEGENA/vignettes/MEGENA_pipeline_10062016.Rmd
MEGENA/MD5
MEGENA/build
MEGENA/build/vignette.rds
MEGENA/DESCRIPTION
MEGENA/man
MEGENA/man/Sample_Expression.Rd
MEGENA/man/calculate.correlation.Rd
MEGENA/man/read.geneSet.Rd
MEGENA/man/MEGENA.ModuleSummary.Rd
MEGENA/man/datExpr.Rd
MEGENA/man/calculate.PFN.Rd
MEGENA/man/get.union.cut.Rd
MEGENA/man/plot_module_hierarchy.Rd
MEGENA/man/plot_subgraph.Rd
MEGENA/man/MEGENA-package.Rd
MEGENA/man/compute.PFN.par.Rd
MEGENA/man/output.geneSet.file.Rd
MEGENA/man/planaritytest.Rd
MEGENA/man/get.hub.summary.Rd
MEGENA/man/do.MEGENA.Rd
MEGENA/man/get.DegreeHubStatistic.Rd
MEGENA/man/plot_module.Rd