CEllular Latent Dirichlet Allocation

Documentation for package ‘celda’ version 1.24.0

Help Pages

-- A --

appendCeldaList	Append two celdaList objects
availableModels	available models

-- B --

bestLogLikelihood	Get the log-likelihood
bestLogLikelihood-method	Get the log-likelihood

-- C --

celda	Celda models
celdaCGGridSearchRes	celdaCGGridSearchRes
celdaCGMod	celdaCGmod
celdaCGSim	celdaCGSim
celdaClusters	Get or set the cell cluster labels from a celda SingleCellExperiment object or celda model object.
celdaClusters-method	Get or set the cell cluster labels from a celda SingleCellExperiment object or celda model object.
celdaClusters<-	Get or set the cell cluster labels from a celda SingleCellExperiment object or celda model object.
celdaClusters<--method	Get or set the cell cluster labels from a celda SingleCellExperiment object or celda model object.
celdaCMod	celdaCMod
celdaCSim	celdaCSim
celdaGMod	celdaGMod
celdaGridSearch	Run Celda in parallel with multiple parameters
celdaGridSearch-method	Run Celda in parallel with multiple parameters
celdaGSim	celdaGSim
celdaHeatmap	Plot celda Heatmap
celdaHeatmap-method	Plot celda Heatmap
celdaModel	Get celda model from a celda SingleCellExperiment object
celdaModel-method	Get celda model from a celda SingleCellExperiment object
celdaModules	Get or set the feature module labels from a celda SingleCellExperiment object.
celdaModules-method	Get or set the feature module labels from a celda SingleCellExperiment object.
celdaModules<-	Get or set the feature module labels from a celda SingleCellExperiment object.
celdaModules<--method	Get or set the feature module labels from a celda SingleCellExperiment object.
celdaPerplexity	Get perplexity for every model in a celdaList
celdaPerplexity-method	Get perplexity for every model in a celdaList
celdaProbabilityMap	Probability map for a celda model
celdaProbabilityMap-method	Probability map for a celda model
celdatosce	Convert old celda model object to 'SCE' object
celdatosce-method	Convert old celda model object to 'SCE' object
celdaTsne	t-Distributed Stochastic Neighbor Embedding (t-SNE) dimension reduction for celda 'sce' object
celdaTsne-method	t-Distributed Stochastic Neighbor Embedding (t-SNE) dimension reduction for celda 'sce' object
celdaUmap	Uniform Manifold Approximation and Projection (UMAP) dimension reduction for celda 'sce' object
celdaUmap-method	Uniform Manifold Approximation and Projection (UMAP) dimension reduction for celda 'sce' object
celda_C	Cell clustering with Celda
celda_C-method	Cell clustering with Celda
celda_CG	Cell and feature clustering with Celda
celda_CG-method	Cell and feature clustering with Celda
celda_G	Feature clustering with Celda
celda_G-method	Feature clustering with Celda
clusterProbability	Get the conditional probabilities of cell in subpopulations from celda model
clusterProbability-method	Get the conditional probabilities of cell in subpopulations from celda model
compareCountMatrix	Check count matrix consistency
compareCountMatrix-method	Check count matrix consistency
contaminationSim	contaminationSim
countChecksum	Get the MD5 hash of the count matrix from the celdaList
countChecksum-method	Get the MD5 hash of the count matrix from the celdaList

-- D --

decontX	Contamination estimation with decontX
decontX-method	Contamination estimation with decontX
decontXcounts	Get or set decontaminated counts matrix
decontXcounts-method	Get or set decontaminated counts matrix
decontXcounts<-	Get or set decontaminated counts matrix
decontXcounts<--method	Get or set decontaminated counts matrix
distinctColors	Create a color palette

-- E --

eigenMatMultInt	Fast matrix multiplication for double x int
eigenMatMultNumeric	Fast matrix multiplication for double x double

-- F --

factorizeMatrix	Generate factorized matrices showing each feature's influence on cell / gene clustering
factorizeMatrix-method	Generate factorized matrices showing each feature's influence on cell / gene clustering
fastNormProp	Fast normalization for numeric matrix
fastNormPropLog	Fast normalization for numeric matrix
fastNormPropSqrt	Fast normalization for numeric matrix
featureModuleLookup	Obtain the gene module of a gene of interest
featureModuleLookup-method	Obtain the gene module of a gene of interest
featureModuleTable	Output a feature module table
findMarkersTree	Generate marker decision tree from single-cell clustering output

-- G --

geneSetEnrich	Gene set enrichment
geneSetEnrich-method	Gene set enrichment
getDecisions	Gets cluster estimates using rules generated by 'celda::findMarkersTree'

-- L --

logLikelihood	Calculate the Log-likelihood of a celda model
logLikelihood-method	Calculate the Log-likelihood of a celda model
logLikelihoodHistory	Get log-likelihood history
logLikelihoodHistory-method	Get log-likelihood history

-- M --

matrixNames	Get feature, cell and sample names from a celdaModel
matrixNames-method	Get feature, cell and sample names from a celdaModel
moduleHeatmap	Heatmap for featureModules
moduleHeatmap-method	Heatmap for featureModules

-- N --

nonzero	get row and column indices of none zero elements in the matrix
normalizeCounts	Normalization of count data

-- P --

params	Get parameter values provided for celdaModel creation
params-method	Get parameter values provided for celdaModel creation
perplexity	Calculate the perplexity of a celda model
perplexity-method	Calculate the perplexity of a celda model
plotCeldaViolin	Feature Expression Violin Plot
plotCeldaViolin-method	Feature Expression Violin Plot
plotDecontXContamination	Plots contamination on UMAP coordinates
plotDecontXMarkerExpression	Plots expression of marker genes before and after decontamination
plotDecontXMarkerPercentage	Plots percentage of cells cell types expressing markers
plotDendro	Plots dendrogram of _findMarkersTree_ output
plotDimReduceCluster	Plotting the cell labels on a dimension reduction plot
plotDimReduceCluster-method	Plotting the cell labels on a dimension reduction plot
plotDimReduceFeature	Plotting feature expression on a dimension reduction plot
plotDimReduceFeature-method	Plotting feature expression on a dimension reduction plot
plotDimReduceGrid	Mapping the dimension reduction plot
plotDimReduceGrid-method	Mapping the dimension reduction plot
plotDimReduceModule	Plotting Celda module probability on a dimension reduction plot
plotDimReduceModule-method	Plotting Celda module probability on a dimension reduction plot
plotGridSearchPerplexity	Visualize perplexity of a list of celda models
plotGridSearchPerplexity-method	Visualize perplexity of a list of celda models
plotHeatmap	Plots heatmap based on Celda model
plotMarkerHeatmap	Generate heatmap for a marker decision tree
plotRPC	Visualize perplexity differences of a list of celda models
plotRPC-method	Visualize perplexity differences of a list of celda models

-- R --

recodeClusterY	Recode feature module labels
recodeClusterZ	Recode cell cluster labels
recursiveSplitCell	Recursive cell splitting
recursiveSplitCell-method	Recursive cell splitting
recursiveSplitModule	Recursive module splitting
recursiveSplitModule-method	Recursive module splitting
reorderCelda	Reorder cells populations and/or features modules using hierarchical clustering
reorderCelda-method	Reorder cells populations and/or features modules using hierarchical clustering
reportceldaCG	Generate an HTML report for celda_CG
reportCeldaCGPlotResults	Generate an HTML report for celda_CG
reportCeldaCGRun	Generate an HTML report for celda_CG
resamplePerplexity	Calculate and visualize perplexity of all models in a celdaList
resamplePerplexity-method	Calculate and visualize perplexity of all models in a celdaList
resList	Get final celdaModels from a celda model 'SCE' or celdaList object
resList-method	Get final celdaModels from a celda model 'SCE' or celdaList object
retrieveFeatureIndex	Retrieve row index for a set of features
runParams	Get run parameters from a celda model 'SingleCellExperiment' or 'celdaList' object
runParams-method	Get run parameters from a celda model 'SingleCellExperiment' or 'celdaList' object

-- S --

sampleCells	sampleCells
sampleLabel	Get or set sample labels from a celda SingleCellExperiment object
sampleLabel-method	Get or set sample labels from a celda SingleCellExperiment object
sampleLabel<-	Get or set sample labels from a celda SingleCellExperiment object
sampleLabel<--method	Get or set sample labels from a celda SingleCellExperiment object
sceCeldaC	sceCeldaC
sceCeldaCG	sceCeldaCG
sceCeldaCGGridSearch	sceCeldaCGGridSearch
sceCeldaG	sceCeldaG
selectBestModel	Select best chain within each combination of parameters
selectBestModel-method	Select best chain within each combination of parameters
selectFeatures	Simple feature selection by feature counts
selectFeatures-method	Simple feature selection by feature counts
semiPheatmap	A function to draw clustered heatmaps.
simulateCells	Simulate count data from the celda generative models.
simulateContamination	Simulate contaminated count matrix
splitModule	Split celda feature module
splitModule-method	Split celda feature module
subsetCeldaList	Subset celda model from SCE object returned from 'celdaGridSearch'
subsetCeldaList-method	Subset celda model from SCE object returned from 'celdaGridSearch'

-- T --

topRank

Identify features with the highest influence on clustering.