Package: rcellminer 2.35.0

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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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rcellminer/json (API)

# Install 'rcellminer' in R:

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

Datasets:

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

On BioConductor:rcellminer-2.35.0(bioc 3.24)rcellminer-2.34.0(bioc 3.23)

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

acgh cellbasedassays copynumbervariation geneexpression pharmacogenomics pharmacogenetics mirna cheminformatics visualization software systemsbiology

5.51 score 109 scripts 3 mentions 45 exports 52 dependencies

Last updated from:78d9626cf0. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	230
linux-devel-x86_64	WARNING	299
source / vignettes	OK	348
linux-release-x86_64	WARNING	330
macos-release-arm64	WARNING	195
macos-oldrel-arm64	WARNING	153
windows-devel	WARNING	203
windows-release	WARNING	222
windows-oldrel	WARNING	198
wasm-release	OK	208

Exports:crossCors DrugData getAct getActivityRangeStats getAllFeatureData getBinaryMutationData getColumnQuantiles getDrugActivityData getDrugActivityRange getDrugActivityRepeatData getDrugMoaList getDrugName getESetList getFeatureAnnot getFeatureDataFromMatList getMedSenLineActivity getMinDrugActivityRepeatCor getMoaStr getMoaToCompounds getMolDataMatrices getMolDataType getNumDrugActivityRepeats getNumMissingLines getRepeatAct getRsd getSampleData getSmiles hasMoa initialize isPublic loadCellminerPlotInfo loadNciColorSet MolData parCorPatternComparison patternComparison plotCellMiner plotCellMiner2D plotDrugActivityRepeats plotDrugSets removeMolDataType restrictFeatureMat rowCors searchForNscs selectCorrelatedRows selectCorrelatedRowsFromMatrices

Dependencies:base64enc Biobase BiocGenerics bitops bslib cachem caTools cli commonmark cpp11 digest farver fastmap fontawesome fs generics ggplot2 glue gplots gtable gtools htmltools httpuv isoband jquerylib jsonlite KernSmooth labeling later lifecycle magrittr memoise mime otel promises R6 rappdirs rcellminerData RColorBrewer Rcpp rlang S7 sass scales shiny sourcetools stringi stringr vctrs viridisLite withr xtable

Using rcellminer

Rendered fromrcellminerUsage.Rmdusingknitr::rmarkdown

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

Help page	Topics
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 Version	cmVersion
Calculate cross-correlations with between rows of input matrices	crossCors
Calculate Spearman's correlations with between rows of input matrices	crossCorsSpearman
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 Values	drugDB
NCI60 Molecular Data	elNetMolDataNCI60
Molecular Fingerprint List	fingerprintList
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 matrix	getColumnQuantiles
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 string	getMoaStr
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) Annotation	hasMoa
Returns a DrugData object.	initialize,DrugData-method
Returns a MolData object.	initialize,MolData-method
Check if an NSC ID is public	isPublic
Returns data to plot CellMiner plots	loadCellminerPlotInfo
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 R	plotCellMiner
Make a simple 2d plot using two variables with ggplot2	plotCellMiner2D
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 correlations	rowCors
Search for NSCs	searchForNscs
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

Package: rcellminer 2.35.0

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

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