netmes: Exploratory Analysis of Gene Networks with Netmes, An R package for network-based measures
Version 1.0

This package implements various algorithms for an explanatory analysis of network based evaluation measures to assess network inference algorithms systematically.

AuthorAuthor: Gokmen Altay, Frank Emmert-Streib
Date of publication2013-11-22 16:14:58
MaintainerGokmen Altay <altayscience@gmail.com>
LicenseGPL (>= 3)
Version1.0
URL http://www.bio-complexity.com/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("netmes", repos="http://R-Forge.R-project.org")

Popular man pages

evalnetworks: Computing all the statistics from data of sythetic network
evalnetworksNames: Computing all the statistics from data of biological network
plotDs: TPR for all of the re or ac types of edges
plotMotifs: Print to screen in latex format of motif statistics
readNet: Fetching true network from .sif file
readSifNet: Fetching true biological network from .sif file
visnet: Plotting the inferability of a network with colored edges
See all...

All man pages Function index File listing

Man pages

evalnetworks: Computing all the statistics from data of sythetic network
evalnetworksNames: Computing all the statistics from data of biological network
motifcount3: Motif statistics for regulatory networks
plotDs: TPR for all of the re or ac types of edges
plotMotifs: Print to screen in latex format of motif statistics
readNet: Fetching true network from .sif file
readSifNet: Fetching true biological network from .sif file
sumdeg: Sum of degree calculation for each node
TPRall: TPR for all of the re or ac types of edges
visnet: Plotting the inferability of a network with colored edges

Functions

TPRall Man page Source code
evalnetworks Man page Source code
evalnetworksNames Man page Source code
motifMI Source code
motifcount3 Man page Source code
motifrate Source code
plotDs Man page Source code
plotMotifs Man page Source code
readMI Source code
readNamesMI Source code
readNet Man page Source code
readSifNet Man page Source code
sumdeg Man page Source code
visnet Man page Source code

Files

DESCRIPTION
EXAMPLES.txt
NAMESPACE
R
R/TPRall.R
R/evalnetworks.R
R/evalnetworksNames.R
R/motifMI.R
R/motifcount3.R
R/motifrate.R
R/plotDs.R
R/plotMotifs.R
R/readMI.R
R/readNamesMI.R
R/readNet.R
R/readSifNet.R
R/sumdeg.R
R/visnet.R
data
data/bio
data/bio/1
data/bio/1/mim.exp
data/bio/1/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
data/bio/2
data/bio/2/mim.exp
data/bio/2/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
data/bio/3
data/bio/3/mim.exp
data/bio/3/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
data/bio/4
data/bio/4/mim.exp
data/bio/4/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
data/bio/5
data/bio/5/mim.exp
data/bio/5/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
data/networkDAG.sif
data/networkEcoli.sif
data/syn
data/syn/1
data/syn/1/mim.exp
data/syn/1/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
data/syn/2
data/syn/2/mim.exp
data/syn/2/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
data/syn/3
data/syn/3/mim.exp
data/syn/3/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
data/syn/4
data/syn/4/mim.exp
data/syn/4/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
data/syn/5
data/syn/5/mim.exp
data/syn/5/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
inst
inst/CITATION
inst/doc
inst/doc/netmes-manual.pdf
inst/extdata
inst/extdata/bio
inst/extdata/bio/1
inst/extdata/bio/1/mim.exp
inst/extdata/bio/1/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
inst/extdata/bio/2
inst/extdata/bio/2/mim.exp
inst/extdata/bio/2/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
inst/extdata/bio/3
inst/extdata/bio/3/mim.exp
inst/extdata/bio/3/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
inst/extdata/bio/4
inst/extdata/bio/4/mim.exp
inst/extdata/bio/4/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
inst/extdata/bio/5
inst/extdata/bio/5/mim.exp
inst/extdata/bio/5/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
inst/extdata/networkDAG.sif
inst/extdata/networkEcoli.sif
inst/extdata/syn
inst/extdata/syn/1
inst/extdata/syn/1/mim.exp
inst/extdata/syn/1/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
inst/extdata/syn/2
inst/extdata/syn/2/mim.exp
inst/extdata/syn/2/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
inst/extdata/syn/3
inst/extdata/syn/3/mim.exp
inst/extdata/syn/3/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
inst/extdata/syn/4
inst/extdata/syn/4/mim.exp
inst/extdata/syn/4/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
inst/extdata/syn/5
inst/extdata/syn/5/mim.exp
inst/extdata/syn/5/nn100_nbgr0_hop0.3_bionoise0.05_expnoise0.0_corrnoise0.0_neighAdd_maxExpr1_dataset.txt
man
man/TPRall.Rd
man/evalnetworks.Rd
man/evalnetworksNames.Rd
man/motifcount3.Rd
man/plotDs.Rd
man/plotMotifs.Rd
man/readNet.Rd
man/readSifNet.Rd
man/sumdeg.Rd
man/visnet.Rd
netmes documentation built on May 21, 2017, 1:17 a.m.

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