SuperCurve: RPPA Analysis Package

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Analyze reverse phase protein lysate arrays.

Author
Kevin R. Coombes, Shannon Neeley, Corwin Joy, Jianhua Hu, Keith Baggerly, and P. Roebuck
Date of publication
2015-08-02 23:18:50
Maintainer
"P. Roebuck" <proebuck@mdanderson.org>
License
Artistic-2.0
Version
1.5.15
URLs

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