template:
   params:
     bootswatch: yeti
 
 reference:
 - title: Function Documentation
   desc: Man pages for all functions exported by celda
   contents:
   - '`available_models`'
   - '`calc.perplexity`'
   - '`calc.perplexity2`'
   - '`calculateLoglikFromVariables.celda_C`'
   - '`calculateLoglikFromVariables.celda_CG`'
   - '`calculateLoglikFromVariables.celda_G`'
   - '`calculateLoglikFromVariables`'
   - '`calculatePerplexity.celda_C`'
   - '`calculatePerplexity.celda_CG`'
   - '`calculatePerplexity.celda_G`'
   - '`calculatePerplexity`'
   - '`calculatePerplexityWithResampling`'
   - '`calculateTsne`'
   - '`cC.decomposeCounts`'
   - '`cCG.decomposeCounts`'
   - '`celda`'
   - '`celdaGridSearch`'
   - '`celdaHeatmap.celda_C`'
   - '`celdaHeatmap.celda_CG`'
   - '`celdaHeatmap.celda_G`'
   - '`celdaHeatmap`'
   - '`celdaProbabilityMap.celda_C`'
   - '`celdaProbabilityMap.celda_CG`'
   - '`celdaProbabilityMap`'
   - '`celdaTsne.celda_C`'
   - '`celdaTsne.celda_CG`'
   - '`celdaTsne.celda_G`'
   - '`celdaTsne`'
   - '`celda_C`'
   - '`celda_CG`'
   - '`celda_G`'
   - '`cG.decomposeCounts`'
   - '`clusterProbability.celda_C`'
   - '`clusterProbability.celda_CG`'
   - '`clusterProbability.celda_G`'
   - '`clusterProbability`'
   - '`compareCountMatrix`'
   - '`completeLogLikelihood`'
   - '`differentialExpression`'
   - '`distinct_colors`'
   - '`eigenMatMultInt`'
   - '`factorizeMatrix.celda_C`'
   - '`factorizeMatrix.celda_CG`'
   - '`factorizeMatrix.celda_G`'
   - '`factorizeMatrix`'
   - '`fastNormProp`'
   - '`fastNormPropLog`'
   - '`fastNormPropSqrt`'
   - '`featureModuleLookup.celda_C`'
   - '`featureModuleLookup.celda_CG`'
   - '`featureModuleLookup.celda_G`'
   - '`featureModuleLookup`'
   - '`finalLogLikelihood`'
   - '`moduleHeatmap`'
   - '`normalizeCounts`'
   - '`pbmc_res`'
   - '`pbmc_select`'
   - '`plotDimReduceCluster`'
   - '`plotDimReduceGene`'
   - '`plotDimReduceGrid`'
   - '`plotDimReduceState`'
   - '`plotGridSearchPerplexity.celda_C`'
   - '`plotGridSearchPerplexity.celda_CG`'
   - '`plotGridSearchPerplexity.celda_G`'
   - '`plotGridSearchPerplexity`'
   - '`plotHeatmap`'
   - '`recodeClusterY`'
   - '`recodeClusterZ`'
   - '`runParams`'
   - '`sample.cells`'
   - '`selectBestModel`'
   - '`semi_pheatmap`'
   - '`simulateCells.celda_C`'
   - '`simulateCells.celda_CG`'
   - '`simulateCells.celda_G`'
   - '`simulateCells`'
   - '`subsetCeldaList`'
   - '`topRank`'
 
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   structure:
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     right: github
   components:
     home:
       icon: fa-home fa-lg
       href: index.html
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       href: reference/index.html
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       text: Articles
       menu:
       - text: Analyzing single-cell RNA-seq count data with Celda
         href: articles/celda-analysis.html