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

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
http://www.bio-complexity.com/

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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

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