Package: clusterExperiment
Title: Compare Clusterings for Single-Cell Sequencing
Version: 2.2.0
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"),
	     person("Marla", "Johnson", role = "ctb"))
Author: Elizabeth Purdom [aut, cre, cph], Davide Risso [aut], Marla Johnson [ctb]
Maintainer: Elizabeth Purdom <epurdom@stat.berkeley.edu>
BugReports: https://github.com/epurdom/clusterExperiment/issues
License: Artistic-2.0
Depends: R (>= 3.5.0), SingleCellExperiment, SummarizedExperiment,
        BiocGenerics
Imports: methods, NMF, RColorBrewer, ape (>= 5.0), phylobase, cluster,
        stats, limma, dendextend, howmany, locfdr, matrixStats,
        graphics, parallel, RSpectra, kernlab, stringr, S4Vectors,
        grDevices, Rcpp, HDF5Array (>= 1.7.10), DelayedArray (>=
        0.5.31), edgeR, scales, zinbwave
Suggests: BiocStyle, knitr, testthat, scRNAseq, MAST, Rtsne, scran,
        igraph
VignetteBuilder: knitr
LazyData: false
LazyLoad: false
RoxygenNote: 6.0.1
biocViews: Clustering, RNASeq, Sequencing, Software, SingleCell
Collate: 'AllChecks.R' 'AllClasses.R' 'AllGenerics.R' 'AllHelper.R'
        'AllHelperClusterFunction.R' 'AllHelperFilter.R'
        'JiashinJiCode.R' 'RcppExports.R' 'addClusterings.R'
        'assignUnassigned.R' 'internalClusterFunctions.R'
        'internalFunctions.R' 'builtInClusterFunctions.R'
        'clusterContrasts.R' 'clusterMany.R' 'clusterSingle.R'
        'dataCreation.R' 'deprecateFunctions.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'
        'subsampleClustering.R' 'subsampleLoop.R' 'subset.R'
        'transformFunction.R' 'updateObject.R' 'workflowClusters.R'
LinkingTo: Rcpp
git_url: https://git.bioconductor.org/packages/clusterExperiment
git_branch: RELEASE_3_8
git_last_commit: 05e03ba
git_last_commit_date: 2018-10-30
Date/Publication: 2018-10-30
NeedsCompilation: yes
Packaged: 2018-10-31 01:37:08 UTC; biocbuild
Built: R 3.5.1; x86_64-apple-darwin15.6.0; 2018-10-31 08:39:30 UTC; unix
