DESCRIPTION

Package: clusterExperiment
Title: Compare Clusterings for Single-Cell Sequencing 
Version: 2.23.4
Description: Provides functionality for running and comparing many
    different clusterings of single-cell sequencing data or other large mRNA Expression data sets.
Authors@R: c(person("Elizabeth", "Purdom", email = "epurdom@stat.berkeley.edu",
            role = c("aut", "cre", "cph")),
	     person("Davide","Risso", role = "aut",email = "risso.davide@gmail.com"))
BugReports: https://github.com/epurdom/clusterExperiment/issues
License: Artistic-2.0
Encoding: UTF-8
Depends:
    R (>= 3.6.0),
    SingleCellExperiment,
	SummarizedExperiment (>= 1.15.4),
	BiocGenerics
Imports:
	methods,
	NMF,
	RColorBrewer,
	ape (>= 5.0),
	cluster,
	stats,
	limma,
	locfdr,
	matrixStats,
	graphics,
	parallel,
	BiocSingular,
	kernlab,
	stringr,
	S4Vectors,
	grDevices,
	DelayedArray (>= 0.7.48),
	HDF5Array (>= 1.7.10),
	Matrix,
	Rcpp,
	edgeR,
	scales,
	zinbwave,
	phylobase,
	pracma,
	mbkmeans
Suggests:
	BiocStyle,
	knitr,
	testthat,
	MAST,
	Rtsne,
	scran,
	igraph,
    rmarkdown
VignetteBuilder: knitr
LazyData: false
LazyLoad: false
RoxygenNote: 7.3.1
biocViews: Clustering, RNASeq, Sequencing, Software, SingleCell
Collate: 
    'AllChecks.R'
    'AllClassesCE.R'
    'AllClassesCF.R'
    'AllGenerics.R'
    'AllHelper.R'
    'AllHelperClusterFunction.R'
    'AllHelperDendro.R'
    'AllHelperFilter.R'
    'JiashinJiCode.R'
    'RcppExports.R'
    'addClusterings.R'
    'assignUnassigned.R'
    'subsampleClustering.R'
    'internalDendroFunctions.R'
    'internalClusterFunctions.R'
    'internalFunctions.R'
    'builtInClusterFunctions.R'
    'clusterContrasts.R'
    'clusterMany.R'
    'clusterSingle.R'
    'dataCreation.R'
    'deprecateFunctions.R'
    'getClusterIndex.R'
    'getFeatures.R'
    'getParams.R'
    'getReducedData.R'
    'mainClustering.R'
    'makeBlankData.R'
    'makeConsensus.R'
    'makeDendrogram.R'
    'makeFilterStats.R'
    'makeReducedDims.R'
    'mergeClusters.R'
    'plotBarplot.R'
    'plotClusters.R'
    'plotClustersTable.R'
    'plotClustersWorkflow.R'
    'plotContrastHeatmap.R'
    'plotDendrogram.R'
    'plotFeatureBoxplot.R'
    'plotFeatureScatter.R'
    'plotHeatmap.R'
    'plotReduceDim.R'
    'plottingHelpers.R'
    'rsec.R'
    'seqCluster.R'
    'subsampleLoop.R'
    'subset.R'
    'transformFunction.R'
    'updateObject.R'
    'workflowClusters.R'
LinkingTo: Rcpp