clusterExperiment: Compare clusterings for single-cell sequencing

This package provides functions for running and comparing many different clusterings of single-cell sequencing data.

AuthorElizabeth Purdom [aut, cre, cph], Davide Risso [aut], Marla Johnson [ctb]
Date of publicationNone
MaintainerElizabeth Purdom <epurdom@stat.berkeley.edu>
LicenseArtistic-2.0
Version1.0.0

View on Bioconductor

Functions

addClusters Man page
addClusters,ClusterExperiment,ClusterExperiment-method Man page
addClusters,ClusterExperiment,matrix-method Man page
addClusters,ClusterExperiment,numeric-method Man page
bigPalette Man page
cluster01 Man page
clusterContrasts Man page
clusterContrasts,ClusterExperiment-method Man page
clusterContrasts,vector-method Man page
clusterD Man page
clusterExperiment Man page
ClusterExperiment Man page
[,ClusterExperiment,ANY,ANY,ANY-method Man page
ClusterExperiment-class Man page
clusterExperiment,matrix,ANY-method Man page
ClusterExperiment-methods Man page
clusterExperiment,SummarizedExperiment,character-method Man page
clusterExperiment,SummarizedExperiment,factor-method Man page
clusterExperiment,SummarizedExperiment,matrix-method Man page
clusterExperiment,SummarizedExperiment,numeric-method Man page
clusterInfo Man page
clusterInfo,ClusterExperiment-method Man page
clusterK Man page
clusterLabels Man page
clusterLabels<- Man page
clusterLabels<-,ClusterExperiment,character-method Man page
clusterLabels,ClusterExperiment-method Man page
clusterLegend Man page
clusterLegend<- Man page
clusterLegend<-,ClusterExperiment,list-method Man page
clusterLegend,ClusterExperiment-method Man page
clusterMany Man page
clusterMany,ClusterExperiment-method Man page
clusterMany,list-method Man page
clusterMany,matrix-method Man page
clusterMany,SummarizedExperiment-method Man page
clusterMatrix Man page
clusterMatrix,ClusterExperiment-method Man page
clusterMatrixNamed Man page
clusterMatrixNamed,ClusterExperiment-method Man page
clusterSingle Man page
clusterSingle,ClusterExperiment-method Man page
clusterSingle,ClusterExperiment,missing-method Man page
clusterSingle,matrix-method Man page
clusterSingle,matrix,missing-method Man page
clusterSingle,matrixOrMissing,matrixOrMissing-method Man page
clusterSingle-methods Man page
clusterSingle,SummarizedExperiment,missing-method Man page
clusterTypes Man page
clusterTypes<- Man page
clusterTypes<-,ClusterExperiment,character-method Man page
clusterTypes,ClusterExperiment-method Man page
coClustering Man page
coClustering<- Man page
coClustering<-,ClusterExperiment,matrix-method Man page
coClustering,ClusterExperiment-method Man page
combineMany Man page
combineMany,ClusterExperiment,character-method Man page
combineMany,ClusterExperiment,missing-method Man page
combineMany,ClusterExperiment,numeric-method Man page
combineMany,matrix,missing-method Man page
convertClusterLegend Man page
convertClusterLegend,ClusterExperiment-method Man page
getBestFeatures Man page
getBestFeatures,ClusterExperiment-method Man page
getBestFeatures,matrix-method Man page
makeBlankData Man page
makeDendrogram Man page
makeDendrogram,ClusterExperiment-method Man page
makeDendrogram,matrix-method Man page
mergeClusters Man page
mergeClusters,ClusterExperiment-method Man page
mergeClusters,matrix-method Man page
nClusters Man page
nClusters,ClusterExperiment-method Man page
nFeatures Man page
nFeatures,ClusterExperiment-method Man page
nSamples Man page
nSamples,ClusterExperiment-method Man page
orderSamples Man page
orderSamples<- Man page
orderSamples,ClusterExperiment-method Man page
orderSamples<-,ClusterExperiment,numeric-method Man page
plotClusters Man page
plotClusters,ClusterExperiment,character-method Man page
plotClusters,ClusterExperiment,missing-method Man page
plotClusters,ClusterExperiment,numeric-method Man page
plotClusters,matrix,missing-method Man page
plotCoClustering Man page
plotCoClustering,ClusterExperiment-method Man page
plotDendrogram Man page
plotDendrogram,ClusterExperiment-method Man page
plotHeatmap Man page
plotHeatmap,ClusterExperiment-method Man page
plotHeatmap,matrix-method Man page
plotHeatmap,SummarizedExperiment-method Man page
plottingFunctions Man page
primaryCluster Man page
primaryCluster,ClusterExperiment-method Man page
primaryClusterIndex Man page
primaryClusterIndex<- Man page
primaryClusterIndex,ClusterExperiment-method Man page
primaryClusterIndex<-,ClusterExperiment,numeric-method Man page
primaryClusterNamed Man page
primaryClusterNamed,ClusterExperiment-method Man page
removeClusters Man page
removeClusters,ClusterExperiment,character-method Man page
removeClusters,ClusterExperiment,numeric-method Man page
removeUnclustered Man page
removeUnclustered,ClusterExperiment-method Man page
RSEC Man page
RSEC,ClusterExperiment-method Man page
RSEC,matrix-method Man page
RSEC-methods Man page
RSEC,SummarizedExperiment-method Man page
seqCluster Man page
seqPal1 Man page
seqPal2 Man page
seqPal3 Man page
seqPal4 Man page
seqPal5 Man page
setBreaks Man page
setToCurrent Man page
setToCurrent,ClusterExperiment-method Man page
setToFinal Man page
setToFinal,ClusterExperiment-method Man page
showBigPalette Man page
show,ClusterExperiment-method Man page
showHeatmapPalettes Man page
simCount Man page
simData Man page
subsampleClustering Man page
transform Man page
transformation Man page
transformation,ClusterExperiment-method Man page
transform,ClusterExperiment-method Man page
trueCluster Man page
workflowClusterDetails Man page
workflowClusterDetails,ClusterExperiment-method Man page
workflowClusters Man page
workflowClusters,ClusterExperiment-method Man page
workflowClusterTable Man page
workflowClusterTable,ClusterExperiment-method Man page

Files

clusterExperiment/DESCRIPTION
clusterExperiment/NAMESPACE
clusterExperiment/NEWS
clusterExperiment/R
clusterExperiment/R/AllClasses.R clusterExperiment/R/AllGenerics.R clusterExperiment/R/AllHelper.R clusterExperiment/R/JiashinJiCode.R clusterExperiment/R/addClusters.R clusterExperiment/R/builtInClusterSubsampleFunctions.R clusterExperiment/R/clusterContrasts.R clusterExperiment/R/clusterD.R clusterExperiment/R/clusterLabels.R clusterExperiment/R/clusterMany.R clusterExperiment/R/clusterSingle.R clusterExperiment/R/combineMany.R clusterExperiment/R/dataCreation.R clusterExperiment/R/getFeatures.R clusterExperiment/R/internalFunctions.R clusterExperiment/R/makeBlankData.R clusterExperiment/R/makeDendrogram.R clusterExperiment/R/mergeClusters.R clusterExperiment/R/plotClusters.R clusterExperiment/R/plotHeatmap.R clusterExperiment/R/plottingHelpers.R clusterExperiment/R/rsec.R clusterExperiment/R/seqCluster.R clusterExperiment/R/subsampleClustering.R clusterExperiment/R/transformFunction.R clusterExperiment/R/workflowClusters.R
clusterExperiment/build
clusterExperiment/build/vignette.rds
clusterExperiment/data
clusterExperiment/data/simData.rda
clusterExperiment/inst
clusterExperiment/inst/doc
clusterExperiment/inst/doc/clusterExperimentTutorial.R
clusterExperiment/inst/doc/clusterExperimentTutorial.Rmd
clusterExperiment/inst/doc/clusterExperimentTutorial.html
clusterExperiment/man
clusterExperiment/man/ClusterExperiment-class.Rd clusterExperiment/man/ClusterExperiment-methods.Rd clusterExperiment/man/RSEC.Rd clusterExperiment/man/addClusters.Rd clusterExperiment/man/clusterContrasts.Rd clusterExperiment/man/clusterD.Rd clusterExperiment/man/clusterMany.Rd clusterExperiment/man/clusterSingle.Rd clusterExperiment/man/combineMany.Rd clusterExperiment/man/convertClusterLegend.Rd clusterExperiment/man/getBestFeatures.Rd clusterExperiment/man/makeDendrogram.Rd clusterExperiment/man/mergeClusters.Rd clusterExperiment/man/plotClusters.Rd clusterExperiment/man/plotHeatmap.Rd clusterExperiment/man/plottingFunctions.Rd clusterExperiment/man/seqCluster.Rd clusterExperiment/man/simData.Rd clusterExperiment/man/subsampleClustering.Rd clusterExperiment/man/transform.Rd clusterExperiment/man/workflowClusters.Rd
clusterExperiment/tests
clusterExperiment/tests/testthat
clusterExperiment/tests/testthat.R
clusterExperiment/tests/testthat/create_objects.R
clusterExperiment/tests/testthat/test_RSEC.R
clusterExperiment/tests/testthat/test_clusterMany.R
clusterExperiment/tests/testthat/test_clusterSingle.R
clusterExperiment/tests/testthat/test_combineMany.R
clusterExperiment/tests/testthat/test_constructor.R
clusterExperiment/tests/testthat/test_dendrogram.R
clusterExperiment/tests/testthat/test_getBestFeatures.R
clusterExperiment/tests/testthat/test_internalFunctions.R
clusterExperiment/tests/testthat/test_mergeClusters.R
clusterExperiment/tests/testthat/test_plotting.R
clusterExperiment/vignettes
clusterExperiment/vignettes/bibFile.bib
clusterExperiment/vignettes/clusterExperimentTutorial.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.