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

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
Date of publicationNone
MaintainerAugustin Luna <lunaa@cbio.mskcc.org>, Vinodh Rajapakse <vinodh.rajapakse@nih.gov>
LicenseLGPL-3
Version1.6.0
http://discover.nci.nih.gov/cellminer/

View on Bioconductor

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

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

Files

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

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