clusterExperiment: Compare Clusterings for Single-Cell Sequencing

Provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA Expression data sets.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("clusterExperiment")
AuthorElizabeth Purdom [aut, cre, cph], Davide Risso [aut], Marla Johnson [ctb]
Bioconductor views Clustering RNASeq Sequencing SingleCell Software
Date of publicationNone
MaintainerElizabeth Purdom <epurdom@stat.berkeley.edu>
LicenseArtistic-2.0
Version1.2.0

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
bigPalette Man page
cluster01 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 Man page
[,ClusterExperiment,ANY,ANY,ANY-method Man page
[,ClusterExperiment,ANY,character,ANY-method Man page
[,ClusterExperiment,ANY,logical,ANY-method Man page
[,ClusterExperiment,ANY,numeric,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
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,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

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