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)

Author
David L Gibbs
Date of publication
None
Maintainer
David L Gibbs <gibbsd@ohsu.edu>
License
GPL (>= 2)
Version
1.12.0

View on Bioconductor

Man pages

accessors
Accessors for the proconaNet S4 class
bootstrapProconaNetwork
bootstrapProconaNetwork
buildProconaNetwork
buildProconaNetwork
c2i
c2i
compareNetworksWithFishersExactTest
compareNetworksWithFishersExactTest
compareNetworksWithFishersExactTestProcona
compareNetworksWithFishersExactTestProcona
corBootstrap
corBootstrap
correlationWithPhenotypesHeatMap
correlationWithPhenotypesHeatMap
getFisherMatrix
getFisherMatrix
getPeptideNAs
getPeptideNAs
goStatTest
goStatTest
hclust
Class '"hclust"'
i2c
i2c
i2col
i2col
MMvsPS
Module members vs Peptide Significance
MMvsPSallModules
MMvsPSallModules
moduleMemberCorrelations
moduleMemberCorrelations
modulePhenotypeCorrelations
modulePhenotypeCorrelations
orderMatrixIndex
orderMatrixIndex
peptideConnectivityTest
peptideConnectivityTest
peptideCorrelationTest
peptideCorrelationTest
plotNet
plotNet
ppiPermTest
ppiPermTest
printNet
printNet
ProCoNA_Data
A simulated mass tag data base
proconaNet-class
proconaNet S4 class
procona-package
Peptide co-expression network construction.
proconaVersionFun
Procona Software Version
runningStats
runningStats
subsetModCors
subsetModCors
subsetPeptideData
subsetPeptideData
toPermTest
toPermTest
utri
utri

Files in this package

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