SCENIC (Single Cell rEgulatory Network Inference and Clustering)


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Documentation for package ‘SCENIC’ version 1.1.2-01

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dbLoadingAttempt Object to store SCENIC settings
dbVersion Object to store SCENIC settings
defaultDbNames Default databases by organism
export2scope export2scope
exportsForArboreto exportsForArboreto (alias: exportsForGRNBoost)
geneFiltering geneFiltering
getDatabases Object to store SCENIC settings
getDatabases-method Object to store SCENIC settings
getDatasetInfo Object to store SCENIC settings
getDatasetInfo-method Object to store SCENIC settings
getDbAnnotations getDbAnnotations
getDbTfs getDbTfs
getIntName Object to store SCENIC settings
getIntName-method Object to store SCENIC settings
getOutName Object to store SCENIC settings
getOutName-method Object to store SCENIC settings
getRegulonName getRegulonName
getSettings Object to store SCENIC settings
getSettings-method Object to store SCENIC settings
getTF getTF
importArboreto importArboreto
importAUCfromText importAUCfromText
initializeScenic Object to store SCENIC settings
loadFile Object to store SCENIC settings
loadFile-method Object to store SCENIC settings
loadInt Object to store SCENIC settings
loadInt-method Object to store SCENIC settings
onlyNonDuplicatedExtended onlyNonDuplicatedExtended
plotTsne_AUCellApp plotTsne_AUCellApp
plotTsne_AUCellHtml plotTsne_AUCellHtml
plotTsne_compareSettings plotTsne_compareSettings
plotTsne_rgb plotTsne_rgb
regulonsToGeneLists regulonsToGeneSet
regulon_plotExpression regulon_plotExpression
runCorrelation runCorrelation
runGenie3 runGenie3
runSCENIC_1_coexNetwork2modules runSCENIC_1_coexNetwork2modules
runSCENIC_2_createRegulons runSCENIC_2_createRegulons
runSCENIC_3_scoreCells runSCENIC_3_scoreCells
runSCENIC_4_aucell_binarize runSCENIC_4_aucell_binarize
ScenicOptions Object to store SCENIC settings
ScenicOptions-class Object to store SCENIC settings
selectRegulons selectRegulons
show Object to store SCENIC settings
show-method Object to store SCENIC settings
tsneAUC tsneAUC
viewMotifs viewMotifs