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

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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.

Author
Augustin Luna, Vinodh Rajapakse, Fabricio Sousa
Date of publication
None
Maintainer
Augustin Luna <lunaa@cbio.mskcc.org>, Vinodh Rajapakse <vinodh.rajapakse@nih.gov>
License
LGPL-3
Version
1.6.0
URLs

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