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

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

Author
Author: Gokmen Altay, Frank Emmert-Streib
Date of publication
2013-11-22 16:14:58
Maintainer
Gokmen Altay <altayscience@gmail.com>
License
GPL (>= 3)
Version
1.0
URLs

View on R-Forge

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

Files in this package

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