| e54ca97f |
# Generated by roxygen2: do not edit by hand
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| baffe474 |
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| 05a1113d |
export("celdaClusters<-")
export("celdaModules<-")
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| c256b4af |
export("decontXcounts<-")
export("sampleLabel<-")
export(appendCeldaList)
export(availableModels)
export(bestLogLikelihood)
export(celda)
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| 05a1113d |
export(celdaClusters)
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| c256b4af |
export(celdaGridSearch)
export(celdaHeatmap)
export(celdaModel)
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| 05a1113d |
export(celdaModules)
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| c256b4af |
export(celdaPerplexity)
export(celdaProbabilityMap)
export(celdaTsne)
export(celdaUmap)
export(celda_C)
export(celda_CG)
export(celda_G)
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| 2ec6775a |
export(celdatosce)
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| c256b4af |
export(clusterProbability)
export(compareCountMatrix)
export(countChecksum)
export(decontX)
export(decontXcounts)
export(differentialExpression)
export(distinctColors)
export(factorizeMatrix)
export(featureModuleLookup)
export(featureModuleTable)
export(findMarkersTree)
export(geneSetEnrich)
export(getDecisions)
export(logLikelihood)
export(logLikelihoodHistory)
export(matrixNames)
export(moduleHeatmap)
export(normalizeCounts)
export(params)
export(perplexity)
export(plotCeldaViolin)
export(plotDecontXContamination)
export(plotDecontXMarkerExpression)
export(plotDecontXMarkerPercentage)
export(plotDimReduceCluster)
export(plotDimReduceFeature)
export(plotDimReduceGrid)
export(plotDimReduceModule)
export(plotGridSearchPerplexity)
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| 329ba8b9 |
export(plotGridSearchPerplexityDiff)
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| c256b4af |
export(plotHeatmap)
export(plotMarkerDendro)
export(plotMarkerHeatmap)
export(recodeClusterY)
export(recodeClusterZ)
export(recursiveSplitCell)
export(recursiveSplitModule)
export(resList)
export(resamplePerplexity)
export(retrieveFeatureIndex)
export(runParams)
export(sampleLabel)
export(selectBestModel)
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| 898ab9e0 |
export(selectFeatures)
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| c256b4af |
export(simulateCells)
export(simulateContamination)
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| f9b287b4 |
export(splitModule)
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| 2ec6775a |
export(subsetCeldaList)
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| c256b4af |
export(topRank)
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| 05a1113d |
exportMethods("celdaClusters<-")
exportMethods("celdaModules<-")
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| c256b4af |
exportMethods("decontXcounts<-")
exportMethods("sampleLabel<-")
exportMethods(bestLogLikelihood)
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| 05a1113d |
exportMethods(celdaClusters)
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| c256b4af |
exportMethods(celdaGridSearch)
exportMethods(celdaHeatmap)
exportMethods(celdaModel)
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| 05a1113d |
exportMethods(celdaModules)
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| c256b4af |
exportMethods(celdaPerplexity)
exportMethods(celdaProbabilityMap)
exportMethods(celdaTsne)
exportMethods(celdaUmap)
exportMethods(celda_C)
exportMethods(celda_CG)
exportMethods(celda_G)
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| 2ec6775a |
exportMethods(celdatosce)
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| c256b4af |
exportMethods(clusterProbability)
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| 53bd7c8d |
exportMethods(compareCountMatrix)
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| c256b4af |
exportMethods(countChecksum)
exportMethods(decontX)
exportMethods(decontXcounts)
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| 05a1113d |
exportMethods(differentialExpression)
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| c256b4af |
exportMethods(factorizeMatrix)
exportMethods(featureModuleLookup)
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| 05a1113d |
exportMethods(findMarkersTree)
exportMethods(geneSetEnrich)
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| c256b4af |
exportMethods(logLikelihood)
exportMethods(logLikelihoodHistory)
exportMethods(matrixNames)
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| 05a1113d |
exportMethods(moduleHeatmap)
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| c256b4af |
exportMethods(params)
exportMethods(perplexity)
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| 05a1113d |
exportMethods(plotCeldaViolin)
exportMethods(plotDimReduceCluster)
exportMethods(plotDimReduceFeature)
exportMethods(plotDimReduceGrid)
exportMethods(plotDimReduceModule)
exportMethods(plotGridSearchPerplexity)
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| 329ba8b9 |
exportMethods(plotGridSearchPerplexityDiff)
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| 05a1113d |
exportMethods(recursiveSplitCell)
exportMethods(recursiveSplitModule)
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| c256b4af |
exportMethods(resList)
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| 05a1113d |
exportMethods(resamplePerplexity)
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| c256b4af |
exportMethods(runParams)
exportMethods(sampleLabel)
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| 4ec87fac |
exportMethods(selectBestModel)
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| 898ab9e0 |
exportMethods(selectFeatures)
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| f9b287b4 |
exportMethods(splitModule)
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| 2ec6775a |
exportMethods(subsetCeldaList)
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| 3de9437b |
import(Rcpp)
import(RcppEigen)
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| 5c12967f |
import(SummarizedExperiment)
import(data.table, except = c(melt, shift))
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| a3823d60 |
import(foreach)
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| e3638ca1 |
import(grDevices)
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| 1a8e0909 |
import(graphics)
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| 7890fdf1 |
import(grid)
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| bd53e0fb |
import(uwot)
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| d7196f24 |
importFrom(MAST,FromMatrix)
importFrom(MAST,summary)
importFrom(MAST,zlm)
importFrom(MCMCprecision,fit_dirichlet)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rtsne,Rtsne)
importFrom(S4Vectors,mcols)
importFrom(data.table,as.data.table)
importFrom(digest,digest)
importFrom(doParallel,registerDoParallel)
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| 6e297e50 |
importFrom(enrichR,enrichr)
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| d7196f24 |
importFrom(enrichR,listEnrichrDbs)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,colors)
importFrom(grDevices,hsv)
importFrom(grDevices,rgb2hsv)
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| 7890fdf1 |
importFrom(grid,grid.pretty)
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| d7196f24 |
importFrom(gtable,gtable)
importFrom(gtable,gtable_add_grob)
importFrom(gtable,gtable_height)
importFrom(gtable,gtable_width)
importFrom(matrixStats,logSumExp)
importFrom(methods,.hasSlot)
importFrom(methods,is)
importFrom(methods,new)
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| 16389352 |
importFrom(multipanelfigure,multi_panel_figure)
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| aa3724e8 |
importFrom(plyr,.)
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| d7196f24 |
importFrom(plyr,mapvalues)
importFrom(reshape2,melt)
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| e3638ca1 |
importFrom(scales,brewer_pal)
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| d7196f24 |
importFrom(scales,dscale)
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| 7890fdf1 |
importFrom(scales,hue_pal)
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| d7196f24 |
importFrom(stringi,stri_list2matrix)
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| fd95d0e3 |
importFrom(withr,with_seed)
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| 3ca4b2ad |
useDynLib(celda,"_colSumByGroup")
useDynLib(celda,"_colSumByGroupChange")
useDynLib(celda,"_colSumByGroup_numeric")
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| 77035eeb |
useDynLib(celda,"_perplexityG")
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| 3ca4b2ad |
useDynLib(celda,"_rowSumByGroup")
useDynLib(celda,"_rowSumByGroupChange")
useDynLib(celda,"_rowSumByGroup_numeric")
|
