Package: rcellminer 2.29.0

Augustin Luna

rcellminer: rcellminer: Molecular Profiles, Drug Response, and Chemical Structures 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.

Authors:Augustin Luna, Vinodh Rajapakse, Fabricio Sousa

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rcellminer.pdf |rcellminer.html✨
rcellminer/json (API)
NEWS

# Install 'rcellminer' in R:
install.packages('rcellminer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • Drug_MOA_Key - A data frame with descriptive information for all compound mechanism of action (MOA) abbreviations used in CellMiner.

On BioConductor:rcellminer-2.29.0(bioc 3.21)rcellminer-2.28.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

acghcellbasedassayscopynumbervariationgeneexpressionpharmacogenomicspharmacogeneticsmirnacheminformaticsvisualizationsoftwaresystemsbiology

5.63 score 95 scripts 232 downloads 3 mentions 45 exports 61 dependencies

Last updated 23 days agofrom:6866a6f87b. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxWARNINGOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macWARNINGOct 31 2024

Exports:crossCorsDrugDatagetActgetActivityRangeStatsgetAllFeatureDatagetBinaryMutationDatagetColumnQuantilesgetDrugActivityDatagetDrugActivityRangegetDrugActivityRepeatDatagetDrugMoaListgetDrugNamegetESetListgetFeatureAnnotgetFeatureDataFromMatListgetMedSenLineActivitygetMinDrugActivityRepeatCorgetMoaStrgetMoaToCompoundsgetMolDataMatricesgetMolDataTypegetNumDrugActivityRepeatsgetNumMissingLinesgetRepeatActgetRsdgetSampleDatagetSmileshasMoainitializeisPublicloadCellminerPlotInfoloadNciColorSetMolDataparCorPatternComparisonpatternComparisonplotCellMinerplotCellMiner2DplotDrugActivityRepeatsplotDrugSetsremoveMolDataTyperestrictFeatureMatrowCorssearchForNscsselectCorrelatedRowsselectCorrelatedRowsFromMatrices

Dependencies:base64encBiobaseBiocGenericsbitopsbslibcachemcaToolsclicolorspacecommonmarkcrayondigestfansifarverfastmapfontawesomefsggplot2gluegplotsgtablegtoolshtmltoolshttpuvisobandjquerylibjsonliteKernSmoothlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigpromisesR6rappdirsrcellminerDataRColorBrewerRcpprlangsassscalesshinysourcetoolsstringistringrtibbleutf8vctrsviridisLitewithrxtable

Using rcellminer

Rendered fromrcellminerUsage.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2021-04-12
Started: 2016-02-25

Readme and manuals

Help Manual

Help pageTopics
Display citation message.onAttach
Make sure that rcellminerData is loaded.onLoad
Returns an indexed eSet object from a MolData object eSet list.[[,MolData-method
Assigns an eSet object to a specified position in a MolData object eSet list.[[<-,MolData-method
CellMiner VersioncmVersion
Calculate cross-correlations with between rows of input matricescrossCors
Calculate Spearman's correlations with between rows of input matricescrossCorsSpearman
A data frame with descriptive information for all compound mechanism of action (MOA) abbreviations used in CellMiner.Drug_MOA_Key
Returns a DrugData object.DrugData
An S4 class to represent drug activity and related data recorded for a set of biological samples..DrugData DrugData-class
Returns a DrugData object.DrugData,eSet,eSet,MIAxE-method
CellMiner Drug Response ValuesdrugDB
NCI60 Molecular DataelNetMolDataNCI60
Molecular Fingerprint ListfingerprintList
Returns an eSet object with drug activity data.getAct
Returns an eSet object with drug activity data.getAct,DrugData-method
Returns a table of activity range statistics for a set of compounds.getActivityRangeStats
Returns a list of feature data matrices.getAllFeatureData
Returns a list of feature data matrices.getAllFeatureData,MolData-method
Compute a binary gene mutation data matrix from SNP and other mutation event-level data.getBinaryMutationData
Calculate quantile for the columns in a matrixgetColumnQuantiles
Returns a matrix containing activity (-logGI50) data for a set of compounds.getDrugActivityData
Returns a vector of log activity range values for set of compounds.getDrugActivityRange
Returns a matrix containing repeat activity experiment data for a compound.getDrugActivityRepeatData
Get a list of applicable MOA strings for a drug.getDrugMoaList
Get the drug names for a set of NSC identifiers.getDrugName
Returns a list of eSet objects.getESetList
Returns a list of eSet objects.getESetList,MolData-method
Returns a list of data frames with feature information.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
Extract from a list of matrices the data associated with a set of features.getFeatureDataFromMatList
Returns a vector of median sensitive cell line activity (-logGI50) values for a set of compounds.getMedSenLineActivity
Returns a table indicating, for each compound in a specified set, the least significant correlation and associated p-value between its replicate experiments.getMinDrugActivityRepeatCor
Get MOA stringgetMoaStr
Get a named list mapping MOA classes to associated compound sets.getMoaToCompounds
Returns a list of molecular data type matrices, with rownames in each matrix prefixed with a data type abbreviation.getMolDataMatrices
Get the molecular data type prefixes for a set of features.getMolDataType
Returns a vector indicating the number of drug activity repeat experiments with available data for each member of a set of compounds.getNumDrugActivityRepeats
Returns a vector indicating the number of NCI-60 cell lines with missing activity data for set of compounds.getNumMissingLines
Returns an eSet object with drug repeat activity experiment data.getRepeatAct
Returns an eSet object with drug repeat activity experiment data.getRepeatAct,DrugData-method
Computes the relative standard deviation values with respect to the columns of a matrix or data.frame.getRsd
Returns a data frame with sample information.getSampleData
Returns a data frame with sample information.getSampleData,DrugData-method
Returns a data frame with sample information.getSampleData,MolData-method
Get the SMILES strings for a set of NSC identifiers.getSmiles
Check if NSC has Mechanism of Action (MOA) AnnotationhasMoa
Returns a DrugData object.initialize,DrugData-method
Returns a MolData object.initialize,MolData-method
Check if an NSC ID is publicisPublic
Returns data to plot CellMiner plotsloadCellminerPlotInfo
Returns a 60-element color set that matches the color set used on http://discover.nci.nih.gov/loadNciColorSet
Returns a MolData object.MolData
An S4 class to represent molecular data recorded for a set of biological samples..MolData MolData-class
Returns a MolData object.MolData,list,MIAxE-method
Compare an input pattern against a set of patterns, excluding the predictive effect of a fixed pattern or set of patterns.parCorPatternComparison
Compare an input pattern against a set of patterns.patternComparison
Description: Produces CellMiner-like plots in RplotCellMiner
Make a simple 2d plot using two variables with ggplot2plotCellMiner2D
Plot NCI-60 drug activity profiles for repeat experiments.plotDrugActivityRepeats
Produces a barplot of the average values for a set of NSCs with a error bar (one standard deviation)plotDrugSets
Remove molecular data type prefixes from features.removeMolDataType
Restricts a feature matrix to only include features associated with a specified gene set.restrictFeatureMat
Row-wise correlationsrowCors
Search for NSCssearchForNscs
Select features that are correlated with a given feature (or one or more features from a set of features).selectCorrelatedRows
Select features that are correlated with a given feature (or one or more features from a set of features), merging results from multiple candidate feature matrices.selectCorrelatedRowsFromMatrices