# CEllular Latent Dirichlet Allocation

## Documentation for package ‘celda’ version 1.6.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G L M N P R S T

## -- 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<- | Get or set decontaminated counts matrix
differentialExpression | Differential expression for cell subpopulations using MAST
differentialExpression-method | Differential expression for cell subpopulations using MAST
distinctColors | Create a color palette

## -- E --

eigenMatMultInt | Fast matrix multiplication for double x int

## -- 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
findMarkersTree-method | 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
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
plotGridSearchPerplexityDiff | Visualize perplexity differences of a list of celda models
plotGridSearchPerplexityDiff-method | Visualize perplexity differences of a list of celda models
plotHeatmap | Plots heatmap based on Celda model
plotMarkerDendro | Plots dendrogram of _findMarkersTree_ output
plotMarkerHeatmap | Generate heatmap for a marker decision tree

## -- 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
resamplePerplexity | Calculate and visualize perplexity of all models in a celdaList, with count resampling
resamplePerplexity-method | Calculate and visualize perplexity of all models in a celdaList, with count resampling
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.