SuperCurve: RPPA Analysis Package

Analyze reverse phase protein lysate arrays.

AuthorKevin R. Coombes, Shannon Neeley, Corwin Joy, Jianhua Hu, Keith Baggerly, and P. Roebuck
Date of publication2015-08-02 23:18:50
Maintainer"P. Roebuck" <proebuck@mdanderson.org>
LicenseArtistic-2.0
Version1.5.15
http://r-forge.r-project.org/projects/supercurve/

View on R-Forge

Man pages

sc00-SuperCurve-package: Reverse phase protein lysate array analysis

sc01-RPPA-class: Class "RPPA"

sc02-RPPADesign-class: Class "RPPADesign" and Class "RPPADesignParams"

sc05-RPPAFit-class: Class "RPPAFit"

sc06-RPPAFitParams-class: Fitting Dilution Curves to Protein Lysate Arrays with Class...

sc07-FitClass-class: Class "FitClass"

sc08-LogisticFitClass-class: Class "LogisticFitClass"

sc09-CobsFitClass-class: Class "CobsFitClass"

sc10-LoessFitClass-class: Class "LoessFitClass"

sc11-RPPASet-class: Class "RPPASet"

sc12-RPPASetSummary-class: Class "RPPASetSummary"

sc13-getConfidenceInterval: Compute Confidence Intervals for a Model Fit to Dilution...

sc14-spatialCorrection: Spatial Correction

sc15-normalize: Normalization

sc19-RPPANormalizationParams-class: Class "RPPANormalizationParams"

sc20-RPPASpatialParams-class: Class "RPPASpatialParams"

sc21-RPPAPreFitQC-class: Class "RPPAPreFitQC"

sc22-DS5RPPAPreFitQC-class: Class "DS5RPPAPreFitQC"

sc70-rppaCell-data: AKT, ERK2, and CTNNB1 expression in cell lines

sc70-rppaSingleSubgrid-data: FOO, BAR, PLUGH, and WALDO expression

sc70-rppaTriple-data: ACTB, CAS3, FAK, and ODC1 expression in 14 fed/starved cell...

sc70-rppaTumor-data: ERK2, GSK3, and JNK expression in tumor samples

sc80-registerModel: Model Registration Methods

sc80-registerNormalizationMethod: Normalization Method Registration Methods

sc90-registrationMethods: Generic Registration Methods

sc98-BoundedRange-class: Class "BoundedRange"

sc98-DefaultProgressMonitor-class: Class "DefaultProgressMonitor"

sc98-Directory-class: Class "Directory"

sc98-ElapsedTime-class: Class "ElapsedTime"

sc98-ProgressMonitor-class: Class "ProgressMonitor"

sc98-ProgressMonitor-methods: Methods for Manipulating Progress Monitors

sc98-SCProgressMonitor-class: Class "SCProgressMonitor"

sc98-SCProgressMonitor-methods: Methods for Manipulating SuperCurve Progress Models

sc98-SuperCurveSettings-class: Class "SuperCurveSettings"

sc99-elapsed-method: Method "elapsed"

sc99-normalize-method: Method "normalize"

sc99-paramString-method: Method "paramString"

sc99-qcprob-method: Method "qcprob"

sc99-write.summary-method: Method "write.summary"

Files in this package

SuperCurve/.aspell
SuperCurve/.aspell/defaults.R
SuperCurve/.aspell/en-antibodies.rds
SuperCurve/.aspell/en-developer.rds
SuperCurve/.aspell/en-microarray.rds
SuperCurve/.aspell/en-software.rds
SuperCurve/.aspell/en-statistics.rds
SuperCurve/DESCRIPTION
SuperCurve/NAMESPACE
SuperCurve/NEWS
SuperCurve/R
SuperCurve/R/AllElapsedTimeGenerics.R SuperCurve/R/AllGenerics.R SuperCurve/R/AllProgressMonitorGenerics.R SuperCurve/R/AllSCProgressMonitorGenerics.R SuperCurve/R/BoundedRange.R SuperCurve/R/Directory-class.R SuperCurve/R/ElapsedTime.R SuperCurve/R/NULL-methods.R SuperCurve/R/ProgressMonitor.R SuperCurve/R/SCProgressMonitor.R SuperCurve/R/bisection.search.R SuperCurve/R/readQuantification.R SuperCurve/R/registration.R SuperCurve/R/sc1-rppa.R SuperCurve/R/sc2-design.R SuperCurve/R/sc3-0-dilutionFitMethods.R SuperCurve/R/sc3-1-dilutionFit.R SuperCurve/R/sc3-2-mainFit.R SuperCurve/R/sc4-normalize.R SuperCurve/R/sc4-spatial.R SuperCurve/R/sc5-rppaSet.R SuperCurve/R/sc6-rppaSetSummary.R SuperCurve/R/sc8-prefitqc.R SuperCurve/R/sc98-settings.R SuperCurve/R/sc99-fitcurve.R SuperCurve/R/utils.R SuperCurve/R/zzz.R
SuperCurve/build
SuperCurve/build/SuperCurve.pdf
SuperCurve/build/vignette.rds
SuperCurve/data
SuperCurve/data/rppaCell.RData
SuperCurve/data/rppaSingleSubgrid.RData
SuperCurve/data/rppaTriple.RData
SuperCurve/data/rppaTumor.RData
SuperCurve/inst
SuperCurve/inst/COPYRIGHTS
SuperCurve/inst/doc
SuperCurve/inst/doc/SuperCurve.R
SuperCurve/inst/doc/SuperCurve.Rnw
SuperCurve/inst/doc/SuperCurve.pdf
SuperCurve/inst/images
SuperCurve/inst/images/missing_slide.tif
SuperCurve/inst/sampleCode
SuperCurve/inst/sampleCode/simExample.R
SuperCurve/inst/sampleCode/supercurveSettings.R
SuperCurve/inst/sampleCode/zz-examples.R
SuperCurve/inst/util
SuperCurve/inst/util/mkRPPACellDataset.R
SuperCurve/inst/util/mkRPPASingleSubgridDataset.R
SuperCurve/inst/util/mkRPPATripleDataset.R
SuperCurve/inst/util/mkRPPATumorDataset.R
SuperCurve/man
SuperCurve/man/sc00-SuperCurve-package.Rd SuperCurve/man/sc01-RPPA-class.Rd SuperCurve/man/sc02-RPPADesign-class.Rd SuperCurve/man/sc05-RPPAFit-class.Rd SuperCurve/man/sc06-RPPAFitParams-class.Rd SuperCurve/man/sc07-FitClass-class.Rd SuperCurve/man/sc08-LogisticFitClass-class.Rd SuperCurve/man/sc09-CobsFitClass-class.Rd SuperCurve/man/sc10-LoessFitClass-class.Rd SuperCurve/man/sc11-RPPASet-class.Rd SuperCurve/man/sc12-RPPASetSummary-class.Rd SuperCurve/man/sc13-getConfidenceInterval.Rd SuperCurve/man/sc14-spatialCorrection.Rd SuperCurve/man/sc15-normalize.Rd SuperCurve/man/sc19-RPPANormalizationParams-class.Rd SuperCurve/man/sc20-RPPASpatialParams-class.Rd SuperCurve/man/sc21-RPPAPreFitQC-class.Rd SuperCurve/man/sc22-DS5RPPAPreFitQC-class.Rd SuperCurve/man/sc70-rppaCell-data.Rd SuperCurve/man/sc70-rppaSingleSubgrid-data.Rd SuperCurve/man/sc70-rppaTriple-data.Rd SuperCurve/man/sc70-rppaTumor-data.Rd SuperCurve/man/sc80-registerModel.Rd SuperCurve/man/sc80-registerNormalizationMethod.Rd SuperCurve/man/sc90-registrationMethods.Rd SuperCurve/man/sc98-BoundedRange-class.Rd SuperCurve/man/sc98-DefaultProgressMonitor-class.Rd SuperCurve/man/sc98-Directory-class.Rd SuperCurve/man/sc98-ElapsedTime-class.Rd SuperCurve/man/sc98-ProgressMonitor-class.Rd SuperCurve/man/sc98-ProgressMonitor-methods.Rd SuperCurve/man/sc98-SCProgressMonitor-class.Rd SuperCurve/man/sc98-SCProgressMonitor-methods.Rd SuperCurve/man/sc98-SuperCurveSettings-class.Rd SuperCurve/man/sc99-elapsed-method.Rd SuperCurve/man/sc99-normalize-method.Rd SuperCurve/man/sc99-paramString-method.Rd SuperCurve/man/sc99-qcprob-method.Rd SuperCurve/man/sc99-write.summary-method.Rd
SuperCurve/tests
SuperCurve/tests/checkFuncs
SuperCurve/tests/sessionInfo.R
SuperCurve/tests/sessionInfo.Rout.save
SuperCurve/tests/testCobs.R
SuperCurve/tests/testCobs.Rout.save
SuperCurve/tests/testDesign.R
SuperCurve/tests/testDesign.Rout.save
SuperCurve/tests/testFit.R
SuperCurve/tests/testFit.Rout.save
SuperCurve/tests/testLoess.R
SuperCurve/tests/testLoess.Rout.save
SuperCurve/tests/testLogistic.R
SuperCurve/tests/testLogistic.Rout.save
SuperCurve/tests/testNormalize.R
SuperCurve/tests/testRPPA.R
SuperCurve/tests/testRPPA.Rout.save
SuperCurve/tests/testRPPANormalizationParams.R
SuperCurve/tests/testRPPANormalizationParams.Rout.save
SuperCurve/tests/testRPPASet.R
SuperCurve/tests/testRPPASet.Rout.save
SuperCurve/tests/testRPPASpatialParams.R
SuperCurve/tests/testRPPASpatialParams.Rout.save
SuperCurve/tests/testRblock
SuperCurve/vignettes
SuperCurve/vignettes/SuperCurve.Rnw

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

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