Last data update: 2014.03.03
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WGCNA
Package: WGCNA
Version: 1.51
Date: 2016-03-08
Title: Weighted Correlation Network Analysis
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Steve Horvath <SHorvath@mednet.ucla.edu> with contributions by Chaochao Cai, Jun Dong, Jeremy Miller, Lin Song, Andy Yip, and Bin Zhang
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Depends: R (>= 3.0), dynamicTreeCut (>= 1.62), fastcluster
Imports: stats, grDevices, utils, matrixStats (>= 0.8.1), Hmisc,
impute, splines, foreach, doParallel, preprocessCore, survival,
parallel, GO.db, AnnotationDbi
Suggests: org.Hs.eg.db, org.Mm.eg.db, infotheo, entropy, minet
ZipData: no
License: GPL (>= 2)
Description: Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
URL:
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/
NeedsCompilation: yes
Packaged: 2016-03-14 22:18:51 UTC; plangfelder
Repository: CRAN
Date/Publication: 2016-03-15 00:24:08
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'WGCNA' ...
** package 'WGCNA' successfully unpacked and MD5 sums checked
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DWITH_THREADS -I/usr/local/include -fpic -g -O2 -c bucketApproxSort.cc -o bucketApproxSort.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DWITH_THREADS -I/usr/local/include -fpic -g -O2 -c corFunctions-common.c -o corFunctions-common.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DWITH_THREADS -I/usr/local/include -fpic -g -O2 -c corFunctions-unified.c -o corFunctions-unified.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DWITH_THREADS -I/usr/local/include -fpic -g -O2 -c networkFunctions.c -o networkFunctions.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DWITH_THREADS -I/usr/local/include -fpic -g -O2 -c pivot.c -o pivot.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DWITH_THREADS -I/usr/local/include -fpic -g -O2 -c quantileC.cc -o quantileC.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o WGCNA.so bucketApproxSort.o corFunctions-common.o corFunctions-unified.o networkFunctions.o pivot.o quantileC.o -lpthread -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/WGCNA/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'WGCNA'
finding HTML links ... done
AFcorMI html
BloodLists html
BrainLists html
BrainRegionMarkers html
GOenrichmentAnalysis html
GTOMdist html
ImmunePathwayLists html
PWLists html
SCsLists html
TOMplot html
TOMsimilarity html
TOMsimilarityFromExpr html
TrueTrait html
WGCNA-package html
accuracyMeasures html
addErrorBars html
addGrid html
addGuideLines html
addTraitToMEs html
adjacency html
adjacency.polyReg html
adjacency.splineReg html
alignExpr html
allocateJobs html
allowWGCNAThreads html
automaticNetworkScreening html
automaticNetworkScreeningGS html
bicor html
bicorAndPvalue html
bicovWeights html
blockSize html
blockwiseConsensusModules html
blockwiseIndividualTOMs html
blockwiseModules html
blueWhiteRed html
branchEigengeneDissim html
branchSplit html
branchSplit.dissim html
branchSplitFromStabilityLabels html
checkAdjMat html
checkSets html
chooseOneHubInEachModule html
chooseTopHubInEachModule html
clusterCoef html
coClustering html
coClustering.permutationTest html
colQuantileC html
collapseRows html
collapseRowsUsingKME html
collectGarbage html
conformityBasedNetworkConcepts html
conformityDecomposition html
consensusDissTOMandTree html
consensusKME html
consensusMEDissimilarity html
consensusOrderMEs html
consensusProjectiveKMeans html
consensusRepresentatives html
consensusTOM html
cor html
corAndPvalue html
corPredictionSuccess html
corPvalueFisher html
corPvalueStudent html
correlationPreservation html
coxRegressionResiduals html
cutreeStatic html
cutreeStaticColor html
displayColors html
dynamicMergeCut html
empiricalBayesLM html
exportNetworkToCytoscape html
exportNetworkToVisANT html
fixDataStructure html
formatLabels html
fundamentalNetworkConcepts html
goodGenes html
goodGenesMS html
goodSamples html
goodSamplesGenes html
goodSamplesGenesMS html
goodSamplesMS html
greenBlackRed html
greenWhiteRed html
hubGeneSignificance html
initProgInd html
intramodularConnectivity html
isMultiData html
kMEcomparisonScatterplot html
keepCommonProbes html
labelPoints html
labeledBarplot html
labeledHeatmap html
labeledHeatmap.multiPage html
labels2colors html
list2multiData html
lowerTri2matrix html
matchLabels html
matrixToNetwork html
mergeCloseModules html
metaAnalysis html
metaZfunction html
moduleColor.getMEprefix html
moduleEigengenes html
moduleMergeUsingKME html
moduleNumber html
modulePreservation html
mtd.apply html
mtd.mapply html
mtd.rbindSelf html
mtd.setAttr html
mtd.setColnames html
mtd.simplify html
mtd.subset html
multiData html
multiData.eigengeneSignificance html
multiSetMEs html
multiUnion html
mutualInfoAdjacency html
nPresent html
nSets html
nearestCentroidPredictor html
nearestNeighborConnectivity html
nearestNeighborConnectivityMS html
networkConcepts html
networkScreening html
networkScreeningGS html
normalizeLabels html
numbers2colors html
orderBranchesUsingHubGenes html
orderMEs html
overlapTable html
overlapTableUsingKME html
pickHardThreshold html
pickSoftThreshold html
plotClusterTreeSamples html
plotColorUnderTree html
plotCor html
plotDendroAndColors html
plotEigengeneNetworks html
plotMEpairs html
plotMat html
plotModuleSignificance html
plotNetworkHeatmap html
populationMeansInAdmixture html
pquantile html
prepComma html
prependZeros html
preservationNetworkConnectivity html
projectiveKMeans html
propVarExplained html
proportionsInAdmixture html
qvalue html
qvalue.restricted html
randIndex html
rankPvalue html
recutBlockwiseTrees html
recutConsensusTrees html
redWhiteGreen html
relativeCorPredictionSuccess html
removeGreyME html
removePrincipalComponents html
returnGeneSetsAsList html
rgcolors.func html
scaleFreeFitIndex html
scaleFreePlot html
selectFewestConsensusMissing html
setCorrelationPreservation html
shortenStrings html
sigmoidAdjacencyFunction html
signedKME html
signumAdjacencyFunction html
simulateDatExpr html
simulateDatExpr5Modules html
simulateEigengeneNetwork html
simulateModule html
simulateMultiExpr html
simulateSmallLayer html
sizeGrWindow html
softConnectivity html
spaste html
standardColors html
standardScreeningBinaryTrait html
standardScreeningCensoredTime html
standardScreeningNumericTrait html
stdErr html
stratifiedBarplot html
subsetTOM html
swapTwoBranches html
transposeBigData html
unsignedAdjacency html
userListEnrichment html
vectorTOM html
vectorizeMatrix html
verboseBarplot html
verboseBoxplot html
verboseIplot html
verboseScatterplot html
votingLinearPredictor html
** building package indices
** testing if installed package can be loaded
==========================================================================
*
* Package WGCNA 1.51 loaded.
*
* Important note: It appears that your system supports multi-threading,
* but it is not enabled within WGCNA in R.
* To allow multi-threading within WGCNA with all available cores, use
*
* allowWGCNAThreads()
*
* within R. Use disableWGCNAThreads() to disable threading if necessary.
* Alternatively, set the following environment variable on your system:
*
* ALLOW_WGCNA_THREADS=<number_of_processors>
*
* for example
*
* ALLOW_WGCNA_THREADS=4
*
* To set the environment variable in linux bash shell, type
*
* export ALLOW_WGCNA_THREADS=4
*
* before running R. Other operating systems or shells will
* have a similar command to achieve the same aim.
*
==========================================================================
* DONE (WGCNA)
Making 'packages.html' ... done
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