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...

Files in this package

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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