Package: COTAN 2.5.6
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:
COTAN_2.5.6.tar.gz
COTAN_2.5.6.zip(r-4.5)COTAN_2.5.6.zip(r-4.4)COTAN_2.5.6.zip(r-4.3)
COTAN_2.5.6.tgz(r-4.4-any)COTAN_2.5.6.tgz(r-4.3-any)
COTAN_2.5.6.tar.gz(r-4.5-noble)COTAN_2.5.6.tar.gz(r-4.4-noble)
COTAN_2.5.6.tgz(r-4.4-emscripten)COTAN_2.3.6.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/seriph78/cotan/issues
- ERCCraw - Data-sets
- raw.dataset - Data-sets
- test.dataset - Data-sets
- test.dataset.clusters1 - Data-sets
- test.dataset.clusters2 - Data-sets
- vignette.merge.clusters - Data-sets
- vignette.split.clusters - Data-sets
On BioConductor:COTAN-2.5.5(bioc 3.20)COTAN-2.4.3(bioc 3.19)
Last updated 15 days agofrom:d0736f123f
Exports:addClusterizationaddClusterizationCoexaddConditionaddElementToMetaDatasetautomaticCOTANObjectCreationcalculateCoexcalculateGcalculateGDIcalculateGDIGivenCorrcalculateGenesCEcalculateLikelihoodOfObservedcalculatePartialCoexcalculatePDIcalculatePValuecalculateScellsHeatmapPlotcellSizePlotcellsUMAPPlotcellsUniformClusteringcheckClusterUniformitycleancleanPlotsclustersDeltaExpressionclustersMarkersHeatmapPlotclustersSummaryDataclustersSummaryPlotclustersTreePlotcontingencyTablesCOTANdatasetTagsDEAOnClustersdistancesBetweenClustersdropCellsCoexdropClusterizationdropConditiondropGenesCellsdropGenesCoexECDPlotestablishGenesClustersestimateDispersionBisectionestimateDispersionNuBisectionestimateLambdaLinearestimateNuLinearestimateNuLinearByClusterestimatorsAreReadyexpectedContingencyTablesexpectedContingencyTablesNNexpectedPartialContingencyTablesexpectedPartialContingencyTablesNNfindClustersMarkersfindFullyExpressedGenesfindFullyExpressingCellsflagNotFullyExpressedGenesflagNotFullyExpressingCellsfromClustersListGDIPlotgenesCoexSpacegeneSetEnrichmentgenesHeatmapPlotgenesSizePlotgetAllConditionsgetCellsgetCellsCoexgetCellsSizegetClusterizationDatagetClusterizationNamegetClusterizationsgetClustersgetClustersCoexgetColorsVectorgetColumnFromDFgetConditiongetConditionNamegetDimsgetDispersiongetFullyExpressedGenesgetFullyExpressingCellsgetGDIgetGenesgetGenesCoexgetGenesSizegetLambdagetLogNormDatagetMetadataCellsgetMetadataDatasetgetMetadataElementgetMetadataGenesgetMugetNormalizedDatagetNugetNumCellsgetNumExpressedGenesgetNumGenesgetNumOfExpressingCellsgetNuNormDatagetProbabilityOfZerogetRawDatagetZeroOneProjgroupByClustersgroupByClustersListheatmapPlotinitializeMetaDatasetisCoexAvailablelogFoldChangeOnClusterslogThismat2vec_rfastmergeClustersmergeUniformCellsClustersmitochondrialPercentagePlotmultiMergeClustersnormalizeNameAndLabelsobservedContingencyTablesobservedContingencyTablesYYobservedPartialContingencyTablesobservedPartialContingencyTablesYYplotThemeproceedToCoexpValueFromDEAreorderClusterizationscatterPlotscCOTANsetColumnInDFsetLoggingFilesetLoggingLevelstoreGDItoClustersListUMAPPlotvec2mat_rfast
Dependencies:abindaskpassassertthatbase64encbeachmatBHBiocGenericsBiocParallelBiocSingularbitopsbslibcachemcaToolscirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDelayedMatrixStatsdeldirdendextenddigestdoParalleldotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGetoptLongggplot2ggrepelggridgesggthemesGlobalOptionsglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallelDistparallellypatchworkpbapplyPCAtoolspillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppGSLRcppHNSWRcppParallelRcppProgressRcppTOMLRcppZigguratreshape2reticulateRfastrjsonrlangrmarkdownROCRrprojrootRSpectrarsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscattermoresctransformSeuratSeuratObjectshapeshinysitmosnowsourcetoolsspspamSparseArraysparseMatrixStatsspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexumaputf8uwotvctrsviridisviridisLitewithrxfunxtableXVectoryamlzeallotzlibbioczoo
Readme and manuals
Help Manual
Help page | Topics |
---|---|
_Clusters_ utilities | ClustersList fromClustersList groupByClusters groupByClustersList mergeClusters multiMergeClusters toClustersList |
Definition of the 'COTAN' class | COTAN-class |
Handle legacy 'scCOTAN'-class and related symmetric matrix <-> vector conversions | COTAN-Legacy mat2vec_rfast scCOTAN scCOTAN-class vec2mat_rfast |
'COTAN' shortcuts | automaticCOTANObjectCreation COTAN COTANObjectCreation proceedToCoex proceedToCoex,COTAN-method |
Data-sets | Datasets ERCCraw raw.dataset test.dataset test.dataset.clusters1 test.dataset.clusters2 vignette.merge.clusters vignette.split.clusters |
getColorsVector | getColorsVector |
Calculations of genes statistics | calculateGDI calculateGDIGivenCorr calculateGenesCE calculatePDI calculatePValue establishGenesClusters genesCoexSpace GenesStatistics getGDI getGDI,COTAN-method storeGDI storeGDI,COTAN-method |
Calculating the COEX matrix for genes and cells | calculateCoex 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' objects | addElementToMetaDataset 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 |
Handling cells' _clusterization_ and related functions | addClusterization addClusterization,COTAN-method addClusterizationCoex addClusterizationCoex,COTAN-method cellsUMAPPlot clustersDeltaExpression 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 functions | addCondition addCondition,COTAN-method dropCondition dropCondition,COTAN-method getAllConditions getAllConditions,COTAN-method getCondition getCondition,COTAN-method getConditionName getConditionName,COTAN-method HandlingConditions normalizeNameAndLabels |
Heatmap Plots | cellsHeatmapPlot genesHeatmapPlot heatmapPlot HeatmapPlots plotTheme singleHeatmapDF |
Installing torch R library (on Linux) | Installing_torch |
Logging in the 'COTAN' package | LoggingFunctions logThis setLoggingFile setLoggingLevel |
Numeric Utilities | dispersionBisection funProbZero nuBisection NumericUtilities parallelDispersionBisection parallelNuBisection |
Estimation of the 'COTAN' model's parameters | estimateDispersionBisection 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 cleaning | cellSizePlot 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' accessors | getCells 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 Clusters | cellsUniformClustering checkClusterUniformity GDIPlot isClusterUniform mergeUniformCellsClusters UniformClusters |