rcellminer: rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
Version 1.8.0

The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.

AuthorAugustin Luna, Vinodh Rajapakse, Fabricio Sousa
Bioconductor views CellBasedAssays Cheminformatics CopyNumberVariation GeneExpression Pharmacogenetics Pharmacogenomics Software SystemsBiology Visualization aCGH miRNA
Date of publicationNone
MaintainerAugustin Luna <lunaa@cbio.mskcc.org>, Vinodh Rajapakse <vinodh.rajapakse@nih.gov>
LicenseLGPL-3
Version1.8.0
URL http://discover.nci.nih.gov/cellminer/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rcellminer")

Getting started

Using rcellminer

Popular man pages

drugDB: CellMiner Drug Response Values
getDrugActivityData: Returns a matrix containing activity (-logGI50) data for a...
getDrugName: Get the drug names for a set of NSC identifiers.
getMinDrugActivityRepeatCor: Returns a table indicating, for each compound in a specified...
hasMoa: Check if NSC has Mechanism of Action (MOA) Annotation
initialize-DrugData-method: Returns a DrugData object.
removeMolDataType: Remove molecular data type prefixes from features.
See all...

All man pages Function index File listing

Man pages

cmVersion: CellMiner Version
compareFingerprints: Compare Structure Fingerprints to NCI DTP Compounds
crossCors: Calculate cross-correlations with between rows of input...
crossCorsSpearman: Calculate Spearman's correlations with between rows of input...
DrugData: Returns a DrugData object.
DrugData-class: An S4 class to represent drug activity and related data...
DrugData-eSet-eSet-MIAxE-method: Returns a DrugData object.
drugDB: CellMiner Drug Response Values
Drug_MOA_Key: A data frame with descriptive information for all compound...
elNetMolDataNCI60: NCI60 Molecular Data
fingerprintList: A list of pre-computed fingerprints using getFingeprintList()
getAct: Returns an eSet object with drug activity data.
getAct-DrugData-method: Returns an eSet object with drug activity data.
getActivityRangeStats: Returns a table of activity range statistics for a set of...
getAllFeatureData: Returns a list of feature data matrices.
getAllFeatureData-MolData-method: Returns a list of feature data matrices.
getBinaryMutationData: Compute a binary gene mutation data matrix from SNP and other...
getColumnQuantiles: Calculate quantile for the columns in a matrix
getDrugActivityData: Returns a matrix containing activity (-logGI50) data for a...
getDrugActivityRange: Returns a vector of log activity range values for set of...
getDrugActivityRepeatData: Returns a matrix containing repeat activity experiment data...
getDrugMoaList: Get a list of applicable MOA strings for a drug.
getDrugName: Get the drug names for a set of NSC identifiers.
getESetList: Returns a list of eSet objects.
getESetList-MolData-method: Returns a list of eSet objects.
getFeatureAnnot: Returns a list of data frames with feature information.
getFeatureAnnot-DrugData-method: Returns a list of data frames with feature information.
getFeatureAnnot-MolData-method: Returns a list of data frames with feature information.
getFeatureDataFromMatList: Extract from a list of matrices the data associated with a...
getFingerprintList: Get a list of fingerprints for a set of compounds
getMedSenLineActivity: Returns a vector of median sensitive cell line activity...
getMinDrugActivityRepeatCor: Returns a table indicating, for each compound in a specified...
getMoaStr: Get MOA string
getMoaToCompounds: Get a named list mapping MOA classes to associated compound...
getMolDataMatrices: Returns a list of molecular data type matrices, with rownames...
getMolDataType: Get the molecular data type prefixes for a set of features.
getNumDrugActivityRepeats: Returns a vector indicating the number of drug activity...
getNumMissingLines: Returns a vector indicating the number of NCI-60 cell lines...
getRepeatAct: Returns an eSet object with drug repeat activity experiment...
getRepeatAct-DrugData-method: Returns an eSet object with drug repeat activity experiment...
getRsd: Computes the relative standard deviation values with respect...
getSampleData: Returns a data frame with sample information.
getSampleData-DrugData-method: Returns a data frame with sample information.
getSampleData-MolData-method: Returns a data frame with sample information.
getSmiles: Get the SMILES strings for a set of NSC identifiers.
hasMoa: Check if NSC has Mechanism of Action (MOA) Annotation
initialize-DrugData-method: Returns a DrugData object.
initialize-MolData-method: Returns a MolData object.
isPublic: Check if an NSC ID is public
loadCellminerPlotInfo: Returns data to plot CellMiner plots
loadNciColorSet: Returns a 60-element color set that matches the color set...
MolData: Returns a MolData object.
MolData-class: An S4 class to represent molecular data recorded for a set of...
MolData-list-MIAxE-method: Returns a MolData object.
passRuleOf5: Checks if SMILES passes Lipinski's Rule of 5
passRuleOf5FromNsc: Checks if NSC passes Lipinski's Rule of 5
patternComparison: Compare an input pattern against a set of patterns.
plotCellMiner: Description: Produces CellMiner-like plots in R
plotDrugActivityRepeats: Plot NCI-60 drug activity profiles for repeat experiments.
plotDrugSets: Produces a barplot of the average values for a set of NSCs...
plotStructures: Plot Structures
plotStructuresFromNscs: Plot the structures for NSCs
rcdkplot: Plot molecules
removeMolDataType: Remove molecular data type prefixes from features.
restrictFeatureMat: Restricts a feature matrix to only include features...
rowCors: Row-wise correlations
runShinyApp: Run Shiny App
runShinyComparePlots: Run the Compare Plots Shiny App
runShinyCompareStructures: Run the Compare Structures Shiny App
runShinyCompoundBrowser: Run the Compound Browser
searchForNscs: Search for NSCs
selectCorrelatedRows: Select features that are correlated with a given feature (or...
selectCorrelatedRowsFromMatrices: Select features that are correlated with a given feature (or...
sub-sub-MolData-method: Returns an indexed eSet object from a MolData object eSet...
sub-subset-MolData-method: Assigns an eSet object to a specified position in a MolData...

Functions

.DrugData Man page
.MolData Man page
DrugData Man page
DrugData,eSet,eSet,MIAxE-method Man page
DrugData-class Man page
Drug_MOA_Key Man page
MolData Man page
MolData,list,MIAxE-method Man page
MolData-class Man page
[[,MolData-method Man page
[[<-,MolData-method Man page
cmVersion Man page
compareFingerprints Man page Source code
crossCors Man page Source code
crossCorsSpearman Man page Source code
drugDB Man page
elNetMolDataNCI60 Man page
fingerprintList Man page
getAct Man page
getAct,DrugData-method Man page
getActivityRangeStats Man page Source code
getAllFeatureData Man page
getAllFeatureData,MolData-method Man page
getBinaryMutationData Man page Source code
getColumnQuantiles Man page Source code
getDrugActivityData Man page Source code
getDrugActivityRange Man page Source code
getDrugActivityRepeatData Man page Source code
getDrugMoaList Man page Source code
getDrugName Man page Source code
getESetList Man page
getESetList,MolData-method Man page
getFeatureAnnot Man page
getFeatureAnnot,DrugData-method Man page
getFeatureAnnot,MolData-method Man page
getFeatureDataFromMatList Man page Source code
getFingerprintList Man page Source code
getMedSenLineActivity Man page Source code
getMinDrugActivityRepeatCor Man page Source code
getMoaStr Man page Source code
getMoaToCompounds Man page Source code
getMolDataMatrices Man page Source code
getMolDataType Man page Source code
getNumDrugActivityRepeats Man page Source code
getNumMissingLines Man page Source code
getRepeatAct Man page
getRepeatAct,DrugData-method Man page
getRsd Man page Source code
getSampleData Man page
getSampleData,DrugData-method Man page
getSampleData,MolData-method Man page
getSmiles Man page Source code
hasMoa Man page Source code
initialize,DrugData-method Man page
initialize,MolData-method Man page
isPublic Man page Source code
loadCellminerPlotInfo Man page Source code
loadNciColorSet Man page Source code
onLoad Source code
passRuleOf5 Man page Source code
passRuleOf5FromNsc Man page Source code
patternComparison Man page Source code
plotCellMiner Man page Source code
plotDrugActivityRepeats Man page Source code
plotDrugSets Man page Source code
plotStructures Man page Source code
plotStructuresFromNscs Man page Source code
rcdkplot Man page Source code
removeMolDataType Man page Source code
restrictFeatureMat Man page Source code
rowCors Man page Source code
runShinyApp Man page Source code
runShinyComparePlots Man page Source code
runShinyCompareStructures Man page Source code
runShinyCompoundBrowser Man page Source code
searchForNscs Man page Source code
selectCorrelatedRows Man page Source code
selectCorrelatedRowsFromMatrices Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllGenerics.R
R/DrugData-class.R
R/DrugData-methods.R
R/Drug_MOA_Key.R
R/MolData-class.R
R/MolData-methods.R
R/compareFingerprints.R
R/crossCors.R
R/dataDocumentation.R
R/getActivityRangeStats.R
R/getBinaryMutationData.R
R/getColumnQuantiles.R
R/getDrugActivityData.R
R/getDrugActivityRange.R
R/getDrugActivityRepeatData.R
R/getDrugMoaList.R
R/getDrugName.R
R/getFeatureDataFromMatList.R
R/getFingerprintList.R
R/getMedSenLineActivity.R
R/getMinDrugActivityRepeatCor.R
R/getMoaStr.R
R/getMoaToCompounds.R
R/getMolDataMatrices.R
R/getMolDataType.R
R/getNumDrugActivityRepeats.R
R/getNumMissingLines.R
R/getRsd.R
R/getSmiles.R
R/hasMoa.R
R/isPublic.R
R/loadCellminerPlotInfo.R
R/loadNciColorSet.R
R/passRuleOf5.R
R/passRuleOf5FromNsc.R
R/patternComparison.R
R/plotCellMiner.R
R/plotDrugActivityRepeats.R
R/plotDrugSets.R
R/plotStructures.R
R/plotStructuresFromNscs.R
R/rcdkplot.R
R/rcellminer.R
R/removeMolDataType.R
R/restrictFeatureMat.R
R/rowCors.R
R/runShinyApp.R
R/runShinyComparePlots.R
R/runShinyCompareStructures.R
R/runShinyCompoundBrowser.R
R/searchForNscs.R
R/selectCorrelatedRows.R
R/selectCorrelatedRowsFromMatrices.R
build
build/vignette.rds
data
data/Drug_MOA_Key.RData
data/datalist
data/fingerprintList.RData
inst
inst/CITATION
inst/doc
inst/doc/rcellminerUsage.R
inst/doc/rcellminerUsage.Rmd
inst/doc/rcellminerUsage.html
inst/extdata
inst/extdata/Drug_MOA_Key.txt
inst/shinyComparePlots
inst/shinyComparePlots/config.json
inst/shinyComparePlots/config.json.orig
inst/shinyComparePlots/functions.R
inst/shinyComparePlots/server.R
inst/shinyComparePlots/ui.R
inst/shinyComparePlots/www
inst/shinyComparePlots/www/files
inst/shinyComparePlots/www/files/about.md
inst/shinyComparePlots/www/files/help.md
inst/shinyComparePlots/www/js
inst/shinyComparePlots/www/js/google-analytics.js
inst/shinyComparePlots/www/js/parse_input.js
inst/shinyCompareStructures
inst/shinyCompareStructures/server.R
inst/shinyCompareStructures/ui.R
inst/shinyFormulas
inst/shinyFormulas/server.R
inst/shinyFormulas/ui.R
inst/shinyReprodPlots
inst/shinyReprodPlots/server.R
inst/shinyReprodPlots/ui.R
inst/shinyTemplate
inst/shinyTemplate/config.json
inst/shinyTemplate/functions.R
inst/shinyTemplate/genericTabs.R
inst/shinyTemplate/server.R
inst/shinyTemplate/ui.R
inst/shinyTutorial
inst/shinyTutorial/server.R
inst/shinyTutorial/ui.R
inst/shinyTutorial/www
inst/shinyTutorial/www/help.md
inst/shinyTutorialHeatmap
inst/shinyTutorialHeatmap/server.R
inst/shinyTutorialHeatmap/ui.R
inst/shinyTutorialHeatmap/www
inst/shinyTutorialHeatmap/www/help.md
inst/tests
inst/tests/test_MolPharmTypes.R
inst/tests/test_compareFingerprints.R
inst/tests/test_crossCors.R
inst/tests/test_getActivityRangeStats.R
inst/tests/test_getBinaryMutationData.R
inst/tests/test_getColumnQuantiles.R
inst/tests/test_getDrugActivityData.R
inst/tests/test_getDrugActivityRange.R
inst/tests/test_getDrugActivityRepeatData.R
inst/tests/test_getDrugMoaList.R
inst/tests/test_getDrugName.R
inst/tests/test_getFeatureDataFromMatList.R
inst/tests/test_getFingerprintList.R
inst/tests/test_getMedSenLineActivity.R
inst/tests/test_getMinDrugActivityRepeatCor.R
inst/tests/test_getMoaStr.R
inst/tests/test_getMoaToCompounds.R
inst/tests/test_getMolDataMatrices.R
inst/tests/test_getMolDataType.R
inst/tests/test_getNumDrugActivityRepeats.R
inst/tests/test_getNumMissingLines.R
inst/tests/test_getRsd.R
inst/tests/test_getSmiles.R
inst/tests/test_hasMoa.R
inst/tests/test_isPublic.R
inst/tests/test_loadNciColorSet.R
inst/tests/test_passRuleOf5.R
inst/tests/test_passRuleOf5FromNsc.R
inst/tests/test_patternComparison.R
inst/tests/test_plotCellMiner.R
inst/tests/test_plotDrugActivityRepeats.R
inst/tests/test_plotDrugSets.R
inst/tests/test_plotStructures.R
inst/tests/test_plotStructuresFromNscs.R
inst/tests/test_rcellminer.R
inst/tests/test_removeMolDataType.R
inst/tests/test_restrictFeatureMat.R
inst/tests/test_searchForNscs.R
inst/tests/test_selectCorrelatedRows.R
inst/tests/test_selectCorrelatedRowsFromMatrices.R
man
man/DrugData-class.Rd
man/DrugData-eSet-eSet-MIAxE-method.Rd
man/DrugData.Rd
man/Drug_MOA_Key.Rd
man/MolData-class.Rd
man/MolData-list-MIAxE-method.Rd
man/MolData.Rd
man/cmVersion.Rd
man/compareFingerprints.Rd
man/crossCors.Rd
man/crossCorsSpearman.Rd
man/drugDB.Rd
man/elNetMolDataNCI60.Rd
man/fingerprintList.Rd
man/getAct-DrugData-method.Rd
man/getAct.Rd
man/getActivityRangeStats.Rd
man/getAllFeatureData-MolData-method.Rd
man/getAllFeatureData.Rd
man/getBinaryMutationData.Rd
man/getColumnQuantiles.Rd
man/getDrugActivityData.Rd
man/getDrugActivityRange.Rd
man/getDrugActivityRepeatData.Rd
man/getDrugMoaList.Rd
man/getDrugName.Rd
man/getESetList-MolData-method.Rd
man/getESetList.Rd
man/getFeatureAnnot-DrugData-method.Rd
man/getFeatureAnnot-MolData-method.Rd
man/getFeatureAnnot.Rd
man/getFeatureDataFromMatList.Rd
man/getFingerprintList.Rd
man/getMedSenLineActivity.Rd
man/getMinDrugActivityRepeatCor.Rd
man/getMoaStr.Rd
man/getMoaToCompounds.Rd
man/getMolDataMatrices.Rd
man/getMolDataType.Rd
man/getNumDrugActivityRepeats.Rd
man/getNumMissingLines.Rd
man/getRepeatAct-DrugData-method.Rd
man/getRepeatAct.Rd
man/getRsd.Rd
man/getSampleData-DrugData-method.Rd
man/getSampleData-MolData-method.Rd
man/getSampleData.Rd
man/getSmiles.Rd
man/hasMoa.Rd
man/initialize-DrugData-method.Rd
man/initialize-MolData-method.Rd
man/isPublic.Rd
man/loadCellminerPlotInfo.Rd
man/loadNciColorSet.Rd
man/passRuleOf5.Rd
man/passRuleOf5FromNsc.Rd
man/patternComparison.Rd
man/plotCellMiner.Rd
man/plotDrugActivityRepeats.Rd
man/plotDrugSets.Rd
man/plotStructures.Rd
man/plotStructuresFromNscs.Rd
man/rcdkplot.Rd
man/removeMolDataType.Rd
man/restrictFeatureMat.Rd
man/rowCors.Rd
man/runShinyApp.Rd
man/runShinyComparePlots.Rd
man/runShinyCompareStructures.Rd
man/runShinyCompoundBrowser.Rd
man/searchForNscs.Rd
man/selectCorrelatedRows.Rd
man/selectCorrelatedRowsFromMatrices.Rd
man/sub-sub-MolData-method.Rd
man/sub-subset-MolData-method.Rd
rcellminer.Rproj
tests
tests/runTests.R
vignettes
vignettes/rcellminerUsage.Rmd
vignettes/shinyComparePlots.png
vignettes/shinyCompareStructures.png
vignettes/shinyReprodPlots.png
rcellminer documentation built on May 20, 2017, 9:39 p.m.