ProCoNA: Protein co-expression network analysis (ProCoNA).

Protein co-expression network construction using peptide level data, with statisical analysis. (Journal of Clinical Bioinformatics 2013, 3:11 doi:10.1186/2043-9113-3-11)

AuthorDavid L Gibbs
Date of publicationNone
MaintainerDavid L Gibbs <gibbsd@ohsu.edu>
LicenseGPL (>= 2)
Version1.12.0

View on Bioconductor

Functions

adj Man page
adj<- Man page
adj<-,proconaNet-method Man page
adj,proconaNet-method Man page
bootstrapProconaNetwork Man page
buildProconaNetwork Man page
c2i Man page
colorOrder Man page
colorOrder Man page
colorOrder<- Man page
colorOrder<- Man page
colorOrder<-,proconaNet-method Man page
colorOrder<-,proconaNet-method Man page
colorOrder,proconaNet-method Man page
colorOrder,proconaNet-method Man page
compareNetworksWithFishersExactTest Man page
compareNetworksWithFishersExactTest,character,character,numeric, Man page
compareNetworksWithFishersExactTestProcona Man page
compareNetworksWithFishersExactTestProcona,proconaNet,proconaNet Man page
corBootstrap Man page
correlationWithPhenotypesHeatMap Man page
correlationWithPhenotypesHeatMap,proconaNet,matrix,numeric,chara Man page
dynamicColors Man page
dynamicColors<- Man page
dynamicColors<-,proconaNet-method Man page
dynamicColors,proconaNet-method Man page
getFisherMatrix Man page
getFisherMatrix,character,character,numeric,numeric-method Man page
getPeptideNAs Man page
goStatTest Man page
goStatTest,proconaNet,numeric,data.frame,character,character,cha Man page
hclust-class Man page
i2c Man page
i2col Man page
masstagdb Man page
mergedColors Man page
mergedColors<- Man page
mergedColors<-,proconaNet-method Man page
mergedColors,proconaNet-method Man page
mergedMEs Man page
mergedMEs<- Man page
mergedMEs<-,proconaNet-method Man page
mergedMEs,proconaNet-method Man page
MEs Man page
MEs<- Man page
MEs<-,proconaNet-method Man page
MEs,proconaNet-method Man page
MMvsPS Man page
MMvsPSallModules Man page
MMvsPSallModules,proconaNet,matrix,numeric,character-method Man page
MMvsPS,proconaNet,matrix,numeric,numeric-method Man page
moduleMemberCorrelations Man page
moduleMemberCorrelations,proconaNet,matrix,matrix-method Man page
modulePhenotypeCorrelations Man page
modulePhenotypeCorrelations,proconaNet,matrix-method Man page
net1 Man page
net2 Man page
networkName Man page
networkName<- Man page
networkName<-,proconaNet-method Man page
networkName,proconaNet-method Man page
networkPower Man page
networkPower<- Man page
networkPower<-,proconaNet-method Man page
networkPower,proconaNet-method Man page
networkType Man page
networkType<- Man page
networkType<-,proconaNet-method Man page
networkType,proconaNet-method Man page
orderMatrixIndex Man page
pepnet Man page
pepnet-class Man page
peptideConnectivityTest Man page
peptideConnectivityTest,proconaNet,data.frame,character,characte Man page
peptideCorrelationTest Man page
peptideCorrelationTest,matrix,data.frame,character,character-met Man page
peptideData Man page
peptides Man page
peptides<- Man page
peptides<-,proconaNet-method Man page
peptides,proconaNet-method Man page
pepTree Man page
pepTree<- Man page
pepTree<-,proconaNet-method Man page
pepTree,proconaNet-method Man page
permtest Man page
permtest<- Man page
permtest<-,proconaNet-method Man page
permtest,proconaNet-method Man page
phenotypes Man page
plotNet Man page
power Man page
power<- Man page
power<-,proconaNet-method Man page
power,proconaNet-method Man page
ppiPermTest Man page
ppiPermTest,proconaNet,matrix,data.frame,character,character,dat Man page
printNet Man page
print,proconaNet-method Man page
proconaNet Man page
proconaNet-class Man page
procona-package Man page
proconaVersion Man page
proconaVersion<- Man page
proconaVersionFun Man page
proconaVersion<-,proconaNet-method Man page
proconaVersion,proconaNet-method Man page
runningStats Man page
samples Man page
samples Man page
samples<- Man page
samples<- Man page
samples<-,proconaNet-method Man page
samples,proconaNet-method Man page
samples<-,proconaNet-methods Man page
samples,proconaNet-methods Man page
show,proconaNet-method Man page
subsetModCors Man page
subsetPeptideData Man page
TOM Man page
TOM<- Man page
TOM<-,proconaNet-method Man page
TOM,proconaNet-method Man page
toPermTest Man page
toPermTest,proconaNet,numeric-method Man page
universe Man page
utri Man page

Files

ProCoNA/DESCRIPTION
ProCoNA/NAMESPACE
ProCoNA/NEWS
ProCoNA/R
ProCoNA/R/allClasses.R ProCoNA/R/bootstrapNetwork.R ProCoNA/R/buildNetwork.R ProCoNA/R/conv.R ProCoNA/R/dataSubset.R ProCoNA/R/errorChecking.R ProCoNA/R/matrixUtils.R ProCoNA/R/moduleMemberStats.R ProCoNA/R/netComparison.R ProCoNA/R/pepPlots.R ProCoNA/R/proconaNet_accessors.R ProCoNA/R/statTests.R
ProCoNA/README
ProCoNA/TODO
ProCoNA/build
ProCoNA/build/vignette.rds
ProCoNA/data
ProCoNA/data/ProCoNA_Data.rda
ProCoNA/data/datalist
ProCoNA/inst
ProCoNA/inst/doc
ProCoNA/inst/doc/ProCoNA_Vignette.R
ProCoNA/inst/doc/ProCoNA_Vignette.Rnw
ProCoNA/inst/doc/ProCoNA_Vignette.pdf
ProCoNA/inst/sample_script
ProCoNA/inst/sample_script/procona_pipeline.R
ProCoNA/inst/unitTests
ProCoNA/inst/unitTests/test_peptideCorrelationTest.R
ProCoNA/inst/unitTests/test_ppiPermTest.R
ProCoNA/inst/unitTests/test_toPermTest.R
ProCoNA/man
ProCoNA/man/MMvsPS.Rd ProCoNA/man/MMvsPSallModules.Rd ProCoNA/man/ProCoNA_Data.Rd ProCoNA/man/accessors.Rd ProCoNA/man/bootstrapProconaNetwork.Rd ProCoNA/man/buildProconaNetwork.Rd ProCoNA/man/c2i.Rd ProCoNA/man/compareNetworksWithFishersExactTest.Rd ProCoNA/man/compareNetworksWithFishersExactTestProcona.Rd ProCoNA/man/corBootstrap.Rd ProCoNA/man/correlationWithPhenotypesHeatMap.Rd ProCoNA/man/getFisherMatrix.Rd ProCoNA/man/getPeptideNAs.Rd ProCoNA/man/goStatTest.Rd ProCoNA/man/hclust.Rd ProCoNA/man/i2c.Rd ProCoNA/man/i2col.Rd ProCoNA/man/moduleMemberCorrelations.Rd ProCoNA/man/modulePhenotypeCorrelations.Rd ProCoNA/man/orderMatrixIndex.Rd ProCoNA/man/peptideConnectivityTest.Rd ProCoNA/man/peptideCorrelationTest.Rd ProCoNA/man/plotNet.Rd ProCoNA/man/ppiPermTest.Rd ProCoNA/man/printNet.Rd ProCoNA/man/procona-package.Rd ProCoNA/man/proconaNet-class.Rd ProCoNA/man/proconaVersionFun.Rd ProCoNA/man/runningStats.Rd ProCoNA/man/subsetModCors.Rd ProCoNA/man/subsetPeptideData.Rd ProCoNA/man/toPermTest.Rd ProCoNA/man/utri.Rd
ProCoNA/tests
ProCoNA/tests/runTests.R
ProCoNA/vignettes
ProCoNA/vignettes/ProCoNA_Package_Blerb.docx
ProCoNA/vignettes/ProCoNA_Vignette.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.