clusterExperiment: Compare clusterings for single-cell sequencing

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

Author
Elizabeth Purdom [aut, cre, cph], Davide Risso [aut], Marla Johnson [ctb]
Date of publication
None
Maintainer
Elizabeth Purdom <epurdom@stat.berkeley.edu>
License
Artistic-2.0
Version
1.0.0

View on Bioconductor

Man pages

addClusters
Functions to add/remove clusters to ClusterExperiment
clusterContrasts
Create contrasts for testing DE of a cluster
clusterD
Cluster distance matrix from subsampling
ClusterExperiment-class
Class ClusterExperiment
ClusterExperiment-methods
Helper methods for the ClusterExperiment class
clusterMany
Create a matrix of clustering across values of parameters
clusterSingle
General wrapper method to cluster the data
combineMany
Find sets of samples that stay together across clusterings
convertClusterLegend
Convert clusterLegend into useful formats
getBestFeatures
Function for finding best features associated with clusters
makeDendrogram
Make hierarchy of set of clusters
mergeClusters
Merge clusters based on dendrogram
plotClusters
Visualize cluster assignments across multiple clusterings
plotHeatmap
Heatmap for showing clustering results and more
plottingFunctions
Various functions useful for plotting
RSEC
Resampling-based Sequential Ensemble Clustering
seqCluster
Program for sequentially clustering, removing cluster, and...
simData
Simulated data for running examples
subsampleClustering
Cluster subsamples of the data
transform
Transform the original data in a ClusterExperiment object
workflowClusters
Methods for workflow clusters

Files in this package

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