Last data update: 2014.03.03
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BioNet
Package: BioNet
Type: Package
Title: Routines for the functional analysis of biological networks
Version: 1.32.0
Date: 2015-09-11
Author: Marcus Dittrich and Daniela Beisser
Maintainer: Marcus Dittrich
<marcus.dittrich@biozentrum.uni-wuerzburg.de>
Description: This package provides functions for the integrated
analysis of protein-protein interaction networks and the
detection of functional modules. Different datasets can be
integrated into the network by assigning p-values of
statistical tests to the nodes of the network. E.g. p-values
obtained from the differential expression of the genes from an
Affymetrix array are assigned to the nodes of the network. By
fitting a beta-uniform mixture model and calculating scores
from the p-values, overall scores of network regions can be
calculated and an integer linear programming algorithm
identifies the maximum scoring subnetwork.
License: GPL (>= 2)
Depends: R (>= 2.10.0), graph, RBGL
Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma,
hgu95av2.db, XML
Imports: igraph (>= 1.0.1), AnnotationDbi, Biobase
LazyLoad: yes
URL: http://bionet.bioapps.biozentrum.uni-wuerzburg.de/
biocViews: Microarray, DataImport, GraphAndNetwork, Network,
NetworkEnrichment, GeneExpression, DifferentialExpression
NeedsCompilation: no
Packaged: 2016-05-04 03:41:51 UTC; biocbuild
● BiocViews: DataImport, DifferentialExpression, GeneExpression, GraphAndNetwork, Microarray, Network, NetworkEnrichment
●
10 images,
44 functions,
0 datasets
●
Reverse Depends: 0
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'BioNet' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'BioNet'
finding HTML links ... done
BioNet-package html
aggrPvals html
bumOptim html
compareNetworks html
consensusScores html
fbum html
fbumLL html
fdrThreshold html
fitBumModel html
getCompScores html
getEdgeList html
hist.bum html
largestComp html
largestScoreComp html
loadNetwork.sif html
loadNetwork.tab html
makeNetwork html
mapByVar html
permutateNodes html
piUpper html
plot.bum html
plot3dModule html
plotLLSurface html
plotModule html
print.bum html
pvaluesExample html
readHeinzGraph html
readHeinzTree html
resamplingPvalues html
rmSelfLoops html
runFastHeinz html
runHeinz html
save3dModule html
saveNetwork html
scanFDR html
scoreFunction html
scoreNodes html
scoreOffset html
sortedEdgeList html
subNetwork html
summary.bum html
writeHeinz html
writeHeinzEdges html
writeHeinzNodes html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BioNet)
Making 'packages.html' ... done
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