Package: COTAN 2.7.1

Galfrè Silvia Giulia

COTAN: COexpression Tables ANalysis

Statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts' distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate p-value for the associated independence test. COTAN can also evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Moreover, this approach provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions and becoming a new tool to identify cell-identity marker genes.

Authors:Galfrè Silvia Giulia [aut, cre], Morandin Francesco [aut], Fantozzi Marco [aut], Pietrosanto Marco [aut], Puttini Daniel [aut], Priami Corrado [aut], Cremisi Federico [aut], Helmer-Citterich Manuela [aut]

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

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

Peer review:

Bug tracker:https://github.com/seriph78/cotan/issues

Datasets:

On BioConductor:COTAN-2.7.0(bioc 3.21)COTAN-2.6.0(bioc 3.20)

systemsbiologytranscriptomicsgeneexpressionsinglecell

6.90 score 16 stars 100 scripts 240 downloads 138 exports 197 dependencies

Last updated 10 days agofrom:8b64d1c73a. Checks:ERROR: 2 WARNING: 5. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 12 2024
R-4.5-winWARNINGNov 12 2024
R-4.5-linuxWARNINGNov 12 2024
R-4.4-winWARNINGNov 12 2024
R-4.4-macWARNINGNov 12 2024
R-4.3-winWARNINGNov 12 2024
R-4.3-macERRORNov 12 2024

Exports:addClusterizationaddClusterizationCoexaddConditionaddElementToMetaDatasetautomaticCOTANObjectCreationcalculateCoexcalculateGcalculateGDIcalculateGDIGivenCorrcalculateGenesCEcalculateLikelihoodOfObservedcalculatePartialCoexcalculatePDIcalculatePValuecalculateScalculateThresholdShiftToUniformitycellsHeatmapPlotcellSizePlotcellsUMAPPlotcellsUniformClusteringcheckClusterUniformitycheckersToDFcheckObjIsUniformcleancleanPlotsclustersDeltaExpressionclustersMarkersHeatmapPlotclustersSummaryDataclustersSummaryPlotclustersTreePlotconditionsFromNamescontingencyTablesconvertFromSingleCellExperimentconvertToSingleCellExperimentCOTANdatasetTagsDEAOnClustersdfToCheckersdistancesBetweenClustersdropCellsCoexdropClusterizationdropConditiondropGenesCellsdropGenesCoexECDPlotestablishGenesClustersestimateDispersionBisectionestimateDispersionNuBisectionestimateLambdaLinearestimateNuLinearestimateNuLinearByClusterestimatorsAreReadyexpectedContingencyTablesexpectedContingencyTablesNNexpectedPartialContingencyTablesexpectedPartialContingencyTablesNNfactorToVectorfindClustersMarkersfindFullyExpressedGenesfindFullyExpressingCellsflagNotFullyExpressedGenesflagNotFullyExpressingCellsfromClustersListGDIPlotgenesCoexSpacegeneSetEnrichmentgenesHeatmapPlotgenesSizePlotgetAllConditionsgetCellsgetCellsCoexgetCellsSizegetCheckerThresholdgetClusterizationDatagetClusterizationNamegetClusterizationsgetClustersgetClustersCoexgetColorsVectorgetColumnFromDFgetConditiongetConditionNamegetDimsgetDispersiongetFullyExpressedGenesgetFullyExpressingCellsgetGDIgetGenesgetGenesCoexgetGenesSizegetLambdagetLogNormDatagetMetadataCellsgetMetadataDatasetgetMetadataElementgetMetadataGenesgetMugetNormalizedDatagetNugetNumCellsgetNumExpressedGenesgetNumGenesgetNumOfExpressingCellsgetNuNormDatagetProbabilityOfZerogetRawDatagetZeroOneProjgroupByClustersgroupByClustersListheatmapPlotinitializeMetaDatasetisCoexAvailablelogFoldChangeOnClusterslogThismat2vec_rfastmergeClustersmergeUniformCellsClustersmitochondrialPercentagePlotmultiMergeClustersniceFactorLevelsnormalizeNameAndLabelsobservedContingencyTablesobservedContingencyTablesYYobservedPartialContingencyTablesobservedPartialContingencyTablesYYplotThemeproceedToCoexpValueFromDEAreorderClusterizationscatterPlotsetColumnInDFsetLoggingFilesetLoggingLevelshiftCheckerThresholdsstoreGDItoClustersListUMAPPlotvec2mat_rfast

Dependencies:abindaskpassassertthatassortheadbase64encbeachmatBHBiobaseBiocGenericsBiocParallelBiocSingularbitopsbslibcachemcaToolscirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDelayedMatrixStatsdeldirdendextenddigestdoParalleldotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2ggrepelggridgesggthemesGlobalOptionsglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallelDistparallellypatchworkpbapplyPCAtoolspillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppGSLRcppHNSWRcppParallelRcppProgressRcppTOMLRcppZigguratreshape2reticulateRfastrjsonrlangrmarkdownROCRrprojrootRSpectrarsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscattermoresctransformSeuratSeuratObjectshapeshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArraysparseMatrixStatsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsystensortibbletidyrtidyselecttinytexUCSC.utilsumaputf8uwotvctrsviridisviridisLitewithrxfunxtableXVectoryamlzeallotzlibbioczoo

Readme and manuals

Help Manual

Help pageTopics
_Clusters_ utilitiesClustersList fromClustersList groupByClusters groupByClustersList mergeClusters multiMergeClusters toClustersList
Data class conversionsConversions convertFromSingleCellExperiment convertToSingleCellExperiment
Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversionsclustersDeltaExpression COTAN_coerce_to_scCOTAN COTAN_Legacy mat2vec_rfast scCOTAN-class scCotan_coerce_to_COTAN vec2mat_rfast
'COTAN' shortcutsautomaticCOTANObjectCreation COTAN COTAN_ObjectCreation proceedToCoex proceedToCoex,COTAN-method
Definition of the 'COTAN' classCOTAN-class
Data-setsDatasets ERCCraw raw.dataset test.dataset test.dataset.clusters1 test.dataset.clusters2 vignette.merge.clusters vignette.merge2.clusters vignette.split.clusters
getColorsVectorgetColorsVector
Calculations of genes statisticscalculateGDI calculateGDIGivenCorr calculateGenesCE calculatePDI calculatePValue establishGenesClusters genesCoexSpace GenesStatistics getGDI getGDI,COTAN-method storeGDI storeGDI,COTAN-method
Calculating the COEX matrix for genes and cellscalculateCoex calculateCoex,COTAN-method calculateG calculateLikelihoodOfObserved calculateMu calculatePartialCoex calculateS CalculatingCOEX contingencyTables dropCellsCoex dropCellsCoex,COTAN-method dropGenesCoex dropGenesCoex,COTAN-method expectedContingencyTables expectedContingencyTablesNN expectedPartialContingencyTables expectedPartialContingencyTablesNN getCellsCoex getCellsCoex,COTAN-method getGenesCoex getGenesCoex,COTAN-method getMu isCoexAvailable isCoexAvailable,COTAN-method observedContingencyTables observedContingencyTablesYY observedPartialContingencyTables observedPartialContingencyTablesYY
Handling _meta-data_ in 'COTAN' objectsaddElementToMetaDataset addElementToMetaDataset,COTAN-method datasetTags getColumnFromDF getDims getDims,COTAN-method getMetadataCells getMetadataCells,COTAN-method getMetadataDataset getMetadataDataset,COTAN-method getMetadataElement getMetadataElement,COTAN-method getMetadataGenes getMetadataGenes,COTAN-method HandleMetaData initializeMetaDataset initializeMetaDataset,COTAN-method setColumnInDF
Handle names and factors' levelsconditionsFromNames factorToVector handleNamesSubsets HandleStrings isEmptyName niceFactorLevels
Handling cells' _clusterization_ and related functionsaddClusterization addClusterization,COTAN-method addClusterizationCoex addClusterizationCoex,COTAN-method cellsUMAPPlot clustersMarkersHeatmapPlot clustersSummaryData clustersSummaryPlot clustersTreePlot DEAOnClusters distancesBetweenClusters dropClusterization dropClusterization,COTAN-method estimateNuLinearByCluster estimateNuLinearByCluster,COTAN-method findClustersMarkers geneSetEnrichment getClusterizationData getClusterizationData,COTAN-method getClusterizationName getClusterizationName,COTAN-method getClusterizations getClusterizations,COTAN-method getClusters getClustersCoex getClustersCoex,COTAN-method HandlingClusterizations logFoldChangeOnClusters pValueFromDEA reorderClusterization UMAPPlot
Handling cells' _conditions_ and related functionsaddCondition addCondition,COTAN-method dropCondition dropCondition,COTAN-method getAllConditions getAllConditions,COTAN-method getCondition getCondition,COTAN-method getConditionName getConditionName,COTAN-method HandlingConditions normalizeNameAndLabels
Heatmap PlotscellsHeatmapPlot genesHeatmapPlot heatmapPlot HeatmapPlots plotTheme singleHeatmapDF
Installing torch R library (on Linux)Installing_torch
Logging in the 'COTAN' packageLoggingFunctions logThis setLoggingFile setLoggingLevel
Handling Multi-Core and GPU environmentscanUseTorch handleMultiCore MultiThreading
Numeric UtilitiesdispersionBisection funProbZero nuBisection NumericUtilities parallelDispersionBisection parallelNuBisection
Estimation of the 'COTAN' model's parametersestimateDispersionBisection estimateDispersionBisection,COTAN-method estimateDispersionNuBisection estimateDispersionNuBisection,COTAN-method estimateDispersionNuNlminb estimateDispersionNuNlminb,COTAN-method estimateLambdaLinear estimateLambdaLinear,COTAN-method estimateNuBisection estimateNuBisection,COTAN-method estimateNuLinear estimateNuLinear,COTAN-method estimatorsAreReady getDispersion getDispersion,COTAN-method getLambda getLambda,COTAN-method getLogNormData getNormalizedData getNu getNu,COTAN-method getNuNormData getProbabilityOfZero ParametersEstimations
Raw data cleaningcellSizePlot clean clean,COTAN-method cleanPlots dropGenesCells dropGenesCells,COTAN-method ECDPlot findFullyExpressedGenes findFullyExpressedGenes,COTAN-method findFullyExpressingCells findFullyExpressingCells,COTAN-method flagNotFullyExpressedGenes flagNotFullyExpressedGenes,COTAN-method flagNotFullyExpressingCells flagNotFullyExpressingCells,COTAN-method genesSizePlot getFullyExpressedGenes getFullyExpressedGenes,COTAN-method getFullyExpressingCells getFullyExpressingCells,COTAN-method mitochondrialPercentagePlot RawDataCleaning scatterPlot
Raw data 'COTAN' accessorsgetCells getCells,COTAN-method getCellsSize getCellsSize,COTAN-method getGenes getGenes,COTAN-method getGenesSize getGenesSize,COTAN-method getNumCells getNumCells,COTAN-method getNumExpressedGenes getNumExpressedGenes,COTAN-method getNumGenes getNumGenes,COTAN-method getNumOfExpressingCells getNumOfExpressingCells,COTAN-method getRawData getRawData,COTAN-method getZeroOneProj getZeroOneProj,COTAN-method RawDataGetters
Uniform ClusterscellsUniformClustering checkClusterUniformity GDIPlot mergeUniformCellsClusters UniformClusters
Definition of the *Transcript Uniformity Checker* classesAdvancedGDIUniformityCheck-class BaseUniformityCheck-class calculateThresholdShiftToUniformity calculateThresholdShiftToUniformity,AdvancedGDIUniformityCheck-method calculateThresholdShiftToUniformity,SimpleGDIUniformityCheck-method checkersToDF checkObjIsUniform checkObjIsUniform,AdvancedGDIUniformityCheck-method checkObjIsUniform,SimpleGDIUniformityCheck-method dfToCheckers GDICheck-class getCheckerThreshold getCheckerThreshold,AdvancedGDIUniformityCheck-method getCheckerThreshold,SimpleGDIUniformityCheck-method shiftCheckerThresholds shiftCheckerThresholds,AdvancedGDIUniformityCheck,numeric-method shiftCheckerThresholds,SimpleGDIUniformityCheck,numeric-method SimpleGDIUniformityCheck-class UniformTranscriptCheckers