netbenchmark: Benchmarking of several gene network inference methods
Version 1.8.0

This package implements a benchmarking of several gene network inference algorithms from gene expression data.

Browse man pages Browse package API and functions Browse package files

AuthorPau Bellot, Catharina Olsen, Patrick Meyer, with contributions from Alexandre Irrthum
Bioconductor views GeneExpression GraphAndNetwork Microarray Network NetworkInference
Date of publicationNone
MaintainerPau Bellot <pau.bellot@upc.edu>
LicenseCC BY-NC-SA 4.0
Version1.8.0
URL https://imatge.upc.edu/netbenchmark/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("netbenchmark")

Man pages

aracne.wrap: aracne wrapper function
c3net.wrap: c3net wrapper function
clr.wrap: CLR wrapper function
comp.metr: Compute metrics
datasource.subsample: Subsampling datasource procedure
evaluate: Inference Evaluation
experiments.bench: Noise sensitivity benchmark
GeneNet.wrap: GeneNet wrapper function
Genie3.wrap: Genie3 wrapper function
mrnetb.wrap: mrnetb wrapper function
mrnet.wrap: mrnet wrapper function
mutrank.wrap: Mutual Rank wrapper function
netbenchmark: Benchmarking of several network inference algorithms from...
netbenchmark.data: Benchmarking of several network inference algorithms for your...
netbenchmark-package: Benchmarking of several inference networks methods
noise.bench: Noise sensitivity test
ntb_globals: Available wrappers in the package of the fast methods
pcit.wrap: pcit wrapper function
rate: Inference Validation
RegistrerWrapper: Wrapper (un)registration routine
zsc: Z-score c++ function
zscore.wrap: Zscore wrapper function

Functions

Adj2Edgelist Source code
GeneNet.wrap Man page Source code
Genie3.wrap Man page Source code
RegisterWrapper Man page Source code
UnregisterWrapper Man page Source code
addnoise Source code
aracne.wrap Man page Source code
aupr Man page Source code
auroc Man page Source code
c3net.wrap Man page Source code
clr.wrap Man page Source code
comp.metr Man page
cont Source code
datasource.subsample Man page Source code
evaluate Man page Source code
experiments.bench Man page Source code
fscore Man page Source code
get.pr Source code
get.pr.plot Source code
get.weight.matrix Source code
lin.to.square Source code
mean.pr Man page
mrnet.wrap Man page Source code
mrnetb.wrap Man page Source code
mutrank.wrap Man page Source code
netbenchmark Man page Source code
netbenchmark-package Man page
netbenchmark.data Man page Source code
netbenchmark_rate Man page
netbenchmark_zsc Man page
noise.bench Man page Source code
ntb_globals Man page
onLoad Source code
pcit.wrap Man page Source code
pgfplots.export Source code
pr.compute Man page
pr.plot Man page Source code
rate Man page Source code
results.plot Source code
roc.compute Man page
roc.plot Man page Source code
zsc Man page Source code
zscore.wrap Man page Source code

Files

CHANGES
DESCRIPTION
NAMESPACE
R
R/GeneNet.wrap.R
R/Genie3.wrap.R
R/RcppExports.R
R/RegistrerWrapper.R
R/aracne.wrap.R
R/c3net.wrap.R
R/clr.wrap.R
R/comp.metr.R
R/dataset.subsample.R
R/evaluate.R
R/experiments.bench.R
R/mrnet.wrap.R
R/mrnetb.wrap.R
R/mutrank.wrap.R
R/netbenchmark.R
R/netbenchmark.data.R
R/noise.bench.R
R/on_load.R
R/pcit.wrap.R
R/zscore.wrap.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/netbenchmark.R
inst/doc/netbenchmark.Rmd
inst/doc/netbenchmark.html
inst/unitTests
inst/unitTests/test_datasource.subsample.R
inst/unitTests/test_evaluate.R
man
man/GeneNet.wrap.Rd
man/Genie3.wrap.Rd
man/RegistrerWrapper.Rd
man/aracne.wrap.Rd
man/c3net.wrap.Rd
man/clr.wrap.Rd
man/comp.metr.Rd
man/datasource.subsample.Rd
man/evaluate.Rd
man/experiments.bench.Rd
man/mrnet.wrap.Rd
man/mrnetb.wrap.Rd
man/mutrank.wrap.Rd
man/netbenchmark-package.Rd
man/netbenchmark.Rd
man/netbenchmark.data.Rd
man/noise.bench.Rd
man/ntb_globals.Rd
man/pcit.wrap.Rd
man/rate.Rd
man/zsc.Rd
man/zscore.wrap.Rd
src
src/RcppExports.cpp
src/netbenchmark_init.c
src/rate.cpp
src/zsc.cpp
tests
tests/runTests.R
vignettes
vignettes/netbenchmark.Rmd
netbenchmark documentation built on May 20, 2017, 9:36 p.m.