Package: clusterExperiment 2.25.0

Elizabeth Purdom

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.

Authors:Elizabeth Purdom [aut, cre, cph], Davide Risso [aut]

# Install 'clusterExperiment' in R:

install.packages('clusterExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/epurdom/clusterexperiment/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

fluidigmColData - Subset of fluidigm data
fluidigmData - Subset of fluidigm data
rsecFluidigm - Documentation of rsecFluidigm object
simCount - Simulated data for running examples
simData - Simulated data for running examples
trueCluster - Simulated data for running examples

On BioConductor:clusterExperiment-2.25.0(bioc 3.20)clusterExperiment-2.24.0(bioc 3.19)

bioconductor-package

122 exports 2.53 score 137 dependencies 1 dependents 8 mentions

Last updated 2 months agofrom:b9692d86c3

Exports:addClusterings addToColData algorithmType assignUnassigned bigPalette checkDendrogram clusterContrasts clusterDendrogram ClusterExperiment ClusterFunction clusteringInfo clusterLabels clusterLabels<-clusterLegend clusterLegend<-clusterMany clusterMatrix clusterMatrixColors clusterMatrixNamed clusterSingle clusterTypes clusterTypes<-coClustering coClustering<-colDataClusters combineMany convertClusterLegend convertToDendrogram defaultNDims dendroClusterIndex eraseMergeInfo filterData filterNames getBestFeatures getBuiltInFunction getClusterIndex getClusterManyParams getMergeCorrespond getPostProcessingArgs getReducedData getSingleClusterIndex inputType internalFunctionCheck listBuiltInFilterStats listBuiltInFunctions listBuiltInReducedDims listBuiltInType01 listBuiltInTypeK mainClustering makeBlankData makeConsensus makeDendrogram makeFilterStats makeReducedDims makeRsecFluidigmObject massivePalette mergeClusterIndex mergeClusters mergeCutoff mergeMethod nClusterings nClusters nFeatures nInternalNodes nNodes nodeIds nodeLabels nodeLabels<-nodeMergeInfo nSamples nTips numericalAsCharacter orderSamples orderSamples<-plotBarplot plotClusterLegend plotClusters plotClustersTable plotClustersWorkflow plotCoClustering plotContrastHeatmap plotDendrogram plotFeatureBoxplot plotFeatureScatter plotHeatmap plotReducedDims primaryCluster primaryClusterIndex primaryClusterIndex<-primaryClusterLabel primaryClusterNamed primaryClusterType recolorClusters removeClusterings removeClusters removeUnassigned renameClusters requiredArgs RSEC sampleDendrogram seqCluster seqPal1 seqPal2 seqPal3 seqPal4 seqPal5 setBreaks setToCurrent setToFinal show showHeatmapPalettes showPalette subsampleClustering subsetByCluster tableClusters transformation transformation<-transformData updateObject workflowClusterDetails workflowClusters workflowClusterTable

Dependencies:abind ade4 annotate AnnotationDbi ape askpass beachmat benchmarkme benchmarkmeData BH Biobase BiocGenerics BiocManager BiocParallel BiocSingular Biostrings bit bit64 blob cachem cli cluster ClusterR codetools colorspace cpp11 crayon curl DBI DelayedArray digest doParallel dplyr edgeR fansi farver fastmap foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gmp gridBase gtable HDF5Array hms httr IRanges irlba isoband iterators jsonlite KEGGREST kernlab labeling lambda.r lattice lifecycle limma locfdr locfit magrittr MASS Matrix MatrixGenerics matrixStats mbkmeans memoise mgcv mime munsell nlme NMF openssl phylobase pillar pixmap pkgconfig plogr plyr png pracma prettyunits progress purrr R6 RColorBrewer Rcpp RcppArmadillo registry reshape2 rhdf5 rhdf5filters Rhdf5lib rlang rncl RNeXML rngtools RSQLite rsvd S4Arrays S4Vectors ScaledMatrix scales SingleCellExperiment snow softImpute sp SparseArray statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect UCSC.utils utf8 uuid vctrs viridisLite withr XML xml2 xtable XVector zinbwave zlibbioc

clusterExperiment Vignette

Elizabeth Purdom and Davide Risso

Rendered fromclusterExperimentTutorial.Rmdusingknitr::rmarkdownon Jul 06 2024.

Last update: 2024-04-25
Started: 2016-04-25

Working with Large Datasets

Elizabeth Purdom and Davide Risso

Rendered fromlargeDataSets.Rmdusingknitr::rmarkdownon Jul 06 2024.

Last update: 2019-10-10
Started: 2019-10-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add clusterings to ClusterExperiment object	addClusterings addClusterings,ClusterExperiment,ClusterExperiment-method addClusterings,ClusterExperiment,matrix-method addClusterings,ClusterExperiment,vector-method removeClusterings
Assign unassigned samples to nearest cluster	assignUnassigned assignUnassigned,ClusterExperiment-method removeUnassigned removeUnassigned,ClusterExperiment-method
Create contrasts for testing DE of a cluster	clusterContrasts clusterContrasts,ClusterExperiment-method clusterContrasts,vector-method
Accessing and manipulating the dendrograms	checkDendrogram checkDendrogram,ClusterExperiment,phylo4d,phylo4d-method clusterDendrogram clusterDendrogram,ClusterExperiment-method convertToDendrogram convertToDendrogram,ClusterExperiment-method nInternalNodes nInternalNodes,ClusterExperiment-method nNodes nNodes,ClusterExperiment-method nodeIds nodeIds,ClusterExperiment-method nodeLabels nodeLabels,ClusterExperiment-method nodeLabels<- nodeLabels<-,ClusterExperiment-method nTips nTips,ClusterExperiment-method sampleDendrogram sampleDendrogram,ClusterExperiment-method
Class ClusterExperiment	ClusterExperiment ClusterExperiment,matrixOrHDF5,ANY-method ClusterExperiment,SingleCellExperiment,character-method ClusterExperiment,SingleCellExperiment,factor-method ClusterExperiment,SingleCellExperiment,matrix-method ClusterExperiment,SingleCellExperiment,numeric-method ClusterExperiment,SummarizedExperiment,ANY-method ClusterExperiment-class
Deprecated functions in package 'clusterExperiment'	clusterExperiment-deprecated combineMany combineMany,ANY-method
Helper methods for the ClusterExperiment class	addToColData addToColData,ClusterExperiment-method ClusterExperiment-methods clusteringInfo clusteringInfo,ClusterExperiment-method clusterLabels clusterLabels,ClusterExperiment-method clusterLabels<- clusterLabels<-,ClusterExperiment,character-method clusterLegend clusterLegend,ClusterExperiment-method clusterLegend<- clusterLegend<-,ClusterExperiment,list-method clusterMatrix clusterMatrix,ClusterExperiment-method clusterMatrixColors clusterMatrixColors,ClusterExperiment-method clusterMatrixNamed clusterMatrixNamed,ClusterExperiment-method clusterTypes clusterTypes,ClusterExperiment-method clusterTypes<- clusterTypes<-,ClusterExperiment,character-method coClustering coClustering,ClusterExperiment-method coClustering<- coClustering<-,ClusterExperiment,dsCMatrix-method coClustering<-,ClusterExperiment,matrix-method coClustering<-,ClusterExperiment,numeric-method colDataClusters colDataClusters,ClusterExperiment-method dendroClusterIndex dendroClusterIndex,ClusterExperiment-method nClusterings nClusterings,ClusterExperiment-method nClusters nClusters,ClusterExperiment-method nFeatures nFeatures,ClusterExperiment-method nSamples nSamples,ClusterExperiment-method orderSamples orderSamples,ClusterExperiment-method orderSamples<- orderSamples<-,ClusterExperiment,numeric-method primaryCluster primaryCluster,ClusterExperiment-method primaryClusterIndex primaryClusterIndex,ClusterExperiment-method primaryClusterIndex<- primaryClusterIndex<-,ClusterExperiment,numeric-method primaryClusterLabel primaryClusterLabel,ClusterExperiment-method primaryClusterNamed primaryClusterNamed,ClusterExperiment-method primaryClusterType primaryClusterType,ClusterExperiment-method show show,ClusterExperiment-method transformation transformation,ClusterExperiment-method transformation<- transformation<-,ClusterExperiment,function-method
Helper methods for the ClusterFunction class	algorithmType algorithmType,character-method algorithmType,ClusterFunction-method algorithmType,factor-method algorithmType,list-method ClusterFunction-methods inputType inputType,character-method inputType,ClusterFunction-method inputType,factor-method inputType,list-method requiredArgs requiredArgs,character-method requiredArgs,ClusterFunction-method requiredArgs,factor-method requiredArgs,list-method
Create a matrix of clustering across values of parameters	clusterMany clusterMany,ClusterExperiment-method clusterMany,data.frame-method clusterMany,matrixOrHDF5-method clusterMany,SingleCellExperiment-method clusterMany,SummarizedExperiment-method
General wrapper method to cluster the data	clusterSingle clusterSingle,ClusterExperiment-method clusterSingle,matrixOrHDF5OrNULL-method clusterSingle,SingleCellExperiment-method clusterSingle,SummarizedExperiment-method
Subset of fluidigm data	fluidigmColData fluidigmData
Function for finding best features associated with clusters	getBestFeatures getBestFeatures,ClusterExperiment-method getBestFeatures,matrixOrHDF5-method
getClusterIndex	getClusterIndex getClusterIndex,ClusterExperiment-method getSingleClusterIndex getSingleClusterIndex,ClusterExperiment-method
Get parameter values of clusterMany clusters	getClusterManyParams getClusterManyParams,ClusterExperiment-method
Return matrix from ClusterExperiment with reduced dimensions	defaultNDims defaultNDims,matrixOrHDF5-method defaultNDims,SingleCellExperiment-method filterData filterData,SummarizedExperiment-method filterNames filterNames,SummarizedExperiment-method getReducedData getReducedData,ClusterExperiment-method listBuiltInFilterStats listBuiltInReducedDims makeFilterStats makeFilterStats,ClusterExperiment-method makeFilterStats,matrixOrHDF5-method makeFilterStats,SummarizedExperiment-method makeReducedDims makeReducedDims,ClusterExperiment-method makeReducedDims,matrixOrHDF5-method makeReducedDims,SingleCellExperiment-method makeReducedDims,SummarizedExperiment-method reduceFunctions
Class ClusterFunction	ClusterFunction ClusterFunction,function-method ClusterFunction-class internalFunctionCheck
Built in ClusterFunction options	getBuiltInFunction getBuiltInFunction,character-method listBuiltInFunctions listBuiltInType01 listBuiltInTypeK
Cluster distance matrix from subsampling	getPostProcessingArgs getPostProcessingArgs,ClusterFunction-method mainClustering mainClustering,character-method mainClustering,ClusterFunction-method
Find sets of samples that stay together across clusterings	makeConsensus makeConsensus,ClusterExperiment-method makeConsensus,matrix-method
Make hierarchy of set of clusters	makeDendrogram makeDendrogram,ClusterExperiment-method makeDendrogram,dist-method makeDendrogram,matrixOrHDF5-method
Merge clusters based on dendrogram	eraseMergeInfo eraseMergeInfo,ClusterExperiment-method getMergeCorrespond getMergeCorrespond,ClusterExperiment-method mergeClusterIndex mergeClusterIndex,ClusterExperiment-method mergeClusters mergeClusters,ClusterExperiment-method mergeClusters,matrixOrHDF5-method mergeCutoff mergeCutoff,ClusterExperiment-method mergeMethod mergeMethod,ClusterExperiment-method nodeMergeInfo nodeMergeInfo,ClusterExperiment-method
Convert numeric values to character that sort correctly	numericalAsCharacter
Barplot of 1 or 2 clusterings	plotBarplot plotBarplot,ClusterExperiment-method plotBarplot,matrix-method plotBarplot,vector-method
Visualize cluster assignments across multiple clusterings	plotClusters plotClusters,ClusterExperiment-method plotClusters,matrix-method
Plot heatmap of cross-tabs of 2 clusterings	bubblePlot,table,table-method plotClustersTable plotClustersTable,ClusterExperiment-method plotClustersTable,table-method tableClusters tableClusters,ClusterExperiment-method
A plot of clusterings specific for clusterMany and workflow visualization	plotClustersWorkflow plotClustersWorkflow,ClusterExperiment-method
Plot heatmaps showing significant genes per contrast	plotContrastHeatmap plotContrastHeatmap,ClusterExperiment-method
Plot dendrogram of ClusterExperiment object	plotDendrogram plotDendrogram,ClusterExperiment-method
Plot boxplot of feature values by cluster	plotFeatureBoxplot plotFeatureBoxplot,ClusterExperiment,character-method plotFeatureBoxplot,ClusterExperiment,numeric-method
Plot scatter plot of feature values colored by cluster	plotFeatureScatter plotFeatureScatter,ClusterExperiment,character-method plotFeatureScatter,ClusterExperiment,numeric-method
Heatmap for showing clustering results and more	plotCoClustering plotCoClustering,ClusterExperiment-method plotHeatmap plotHeatmap,ClusterExperiment-method plotHeatmap,data.frame-method plotHeatmap,ExpressionSet-method plotHeatmap,matrixOrHDF5-method plotHeatmap,SingleCellExperiment-method plotHeatmap,SummarizedExperiment-method plotHeatmap,table-method
Plot 2-dimensionsal representation with clusters	plotReducedDims plotReducedDims,ClusterExperiment-method
Convert clusterLegend into useful formats	bigPalette convertClusterLegend convertClusterLegend,ClusterExperiment-method makeBlankData massivePalette plotClusterLegend plotClusterLegend,ClusterExperiment-method plottingFunctions seqPal1 seqPal2 seqPal3 seqPal4 seqPal5 setBreaks showHeatmapPalettes showPalette
Change assigned names or colors of clusters	recolorClusters recolorClusters,ClusterExperiment,character-method renameClusters renameClusters,ClusterExperiment,character-method
Resampling-based Sequential Ensemble Clustering	RSEC RSEC,ClusterExperiment-method RSEC,data.frame-method RSEC,matrix-method RSEC,matrixOrHDF5-method RSEC,SingleCellExperiment-method RSEC,SummarizedExperiment-method RSEC-methods
Documentation of rsecFluidigm object	makeRsecFluidigmObject rsecFluidigm
Search pairs of samples that co-cluster across subsamples	search_pairs
Program for sequentially clustering, removing cluster, and starting again.	seqCluster
Simulated data for running examples	simCount simData trueCluster
Cluster subsamples of the data	subsampleClustering subsampleClustering,character-method subsampleClustering,ClusterFunction-method
Functions to subset ClusterExperiment Objects	removeClusterings,ClusterExperiment-method removeClusters removeClusters,ClusterExperiment-method subset subsetByCluster subsetByCluster,ClusterExperiment-method [,ClusterExperiment,ANY,ANY,ANY-method [,ClusterExperiment,ANY,character,ANY-method [,ClusterExperiment,ANY,logical,ANY-method [,ClusterExperiment,ANY,numeric,ANY-method
Transform the original data in a ClusterExperiment object	transformData transformData,ClusterExperiment-method transformData,matrixOrHDF5-method transformData,SingleCellExperiment-method transformData,SummarizedExperiment-method
Update old ClusterExperiment object to current class definition	updateObject updateObject,ClusterExperiment-method
Methods for workflow clusters	setToCurrent setToCurrent,ClusterExperiment-method setToFinal setToFinal,ClusterExperiment-method workflowClusterDetails workflowClusterDetails,ClusterExperiment-method workflowClusters workflowClusters,ClusterExperiment-method workflowClusterTable workflowClusterTable,ClusterExperiment-method