NAMESPACE

# Generated by roxygen2: do not edit by hand

export(.Annotate4Plotly3D)
export(.getNrCores)
export(Add.DE.combined.score)
export(AddNewAnnotation)
export(AreTheseCellNamesTheSame)
export(AutoLabel.KnownMarkers)
export(AutoLabelTop.logFC)
export(AutoNumber.by.PrinCurve)
export(AutoNumber.by.UMAP)
export(BackupReduction)
export(Calc.Cor.Seurat)
export(CalculateFractionInTrome)
export(Convert10Xfolders)
export(Convert10Xfolders.old)
export(Convert10Xfolders_v1)
export(ConvertDropSeqfolders)
export(Create.MiscSlot)
export(DimPlot.ClusterNames)
export(DiscretePaletteSafe)
export(FindCorrelatedGenes)
export(FlipReductionCoordinates)
export(GetClusteringRuns)
export(GetMostVarGenes)
export(GetNamedClusteringRuns)
export(GetNumberOfClusters)
export(GetOrderedClusteringRuns)
export(GetTopMarkers)
export(GetTopMarkersDF)
export(GetUpdateStats)
export(HGNC.EnforceUnique)
export(IntersectGeneLsWithObject)
export(LoadAllSeurats)
export(PctCellsExpressingGenes)
export(PercentInTranscriptome)
export(Plot3D.ListOfCategories)
export(Plot3D.ListOfGenes)
export(PlotFilters)
export(PlotTopGenes)
export(PlotTopGenesPerCluster)
export(PlotUpdateStats)
export(PrctCellExpringGene)
export(RecallReduction)
export(RemoveGenesSeurat)
export(RenameClustering)
export(RenameGenesSeurat)
export(SavePlotlyAsHtml)
export(SelectHighlyExpressedGenesq99)
export(SetupReductionsNtoKdimensions)
export(SeuratColorVector)
export(SmallestNonAboveX)
export(StoreAllMarkers)
export(StoreTop25Markers)
export(UpdateGenesSeurat)
export(UpdateSeuratObjectProperly)
export(add.meta.tags)
export(addGeneClassFractions)
export(addMetaDataSafe)
export(addMetaFraction)
export(addToMiscOrToolsSlot)
export(addTranslatedMetadata)
export(calc.cluster.averages)
export(calc.q99.Expression.and.set.all.genes)
export(calculateAverageMetaData)
export(calculatePercentageMatch)
export(check.genes)
export(clUMAP)
export(clip10Xcellname)
export(compareVarFeaturesAndRanks)
export(copyCompleteToolsSlots)
export(copyMiscElements)
export(countEnrichedDepletedGenes)
export(countRelevantEnrichments)
export(create.metadata.vector)
export(create_scCombinedMeta)
export(downsampleListSeuObjsNCells)
export(downsampleListSeuObjsPercent)
export(downsampleSeuObj)
export(downsampleSeuObj.and.Save)
export(downsampleSeuObjByIdentAndMaxcells)
export(dropLevelsSeurat)
export(filterCodingGenes)
export(filterExpressedGenes)
export(filterGoEnrichment)
export(find10XoutputFolders)
export(find_prefix_in_cell_IDs)
export(fix.orig.ident)
export(fixZeroIndexing.seurat)
export(gene.name.check)
export(getCellIDs.from.meta)
export(getClusterColors)
export(getClusterNames)
export(getDiscretePalette)
export(getDiscretePaletteObj)
export(getMedianMetric.lsObj)
export(getMetaColnames)
export(getMetadataColumn)
export(get_levels_seu)
export(gg_color_hue)
export(heatmap_calc_clust_median)
export(isave.RDS)
export(isave.image)
export(jJaccardIndexBinary)
export(jJaccardIndexVec)
export(jPairwiseJaccardIndex)
export(jPairwiseJaccardIndexList)
export(jPresenceMatrix)
export(load10Xv3)
export(make10Xcellname)
export(matchBestIdentity)
export(merge_seurat_metadata)
export(metaColnameExists)
export(multiFeaturePlot.A4)
export(multiSingleClusterHighlightPlots.A4)
export(multi_clUMAP.A4)
export(panelCorPearson)
export(parallel.computing.by.future)
export(plot.Gene.Cor.Heatmap)
export(plot.UMAP.tSNE.sidebyside)
export(plot.expression.rank.q90)
export(plot3D.umap)
export(plot3D.umap.gene)
export(plotAndSaveHeatmaps)
export(plotGeneExprHistAcrossCells)
export(plotGeneExpressionInBackgroundHist)
export(plotMetadataCategPie)
export(plotMetadataCorHeatmap)
export(plotMetadataMedianFractionBarplot)
export(plotQUMAPsInAFolder)
export(plotTheSoup)
export(prefix_cells_seurat)
export(processSeuratObject)
export(qClusteringUMAPS)
export(qFeatureScatter)
export(qGeneExpressionUMAPS)
export(qMarkerCheck.BrainOrg)
export(qQC.plots.BrainOrg)
export(qSeuViolin)
export(qUMAP)
export(qqSaveGridA4)
export(qsave.image)
export(read10x)
export(recall.all.genes)
export(recall.genes.ls)
export(recall.meta.tags.n.datasets)
export(recall.parameters)
export(regress_out_and_recalculate_seurat)
export(removeCellsByUmap)
export(removeClustersAndDropLevels)
export(removeLayersByPattern)
export(removeResidualSmallClusters)
export(removeScaleData)
export(renameAzimuthColumns)
export(renameSmallCategories)
export(runDGEA)
export(sampleNpc)
export(save.parameters)
export(save2plots.A4)
export(save4plots.A4)
export(saveLsSeuratMetadata)
export(scBarplot.CellFractions)
export(scBarplot.CellsPerCluster)
export(scBarplot.CellsPerObject)
export(scBarplot.FractionAboveThr)
export(scBarplot.FractionBelowThr)
export(scBarplotEnrichr)
export(scBarplotStackedMetaCateg_List)
export(scCalcPCAVarExplained)
export(scEnhancedVolcano)
export(scGOEnrichment)
export(scPlotPCAvarExplained)
export(set.mm)
export(seu.Make.Cl.Label.per.cell)
export(seu.RemoveMetadata)
export(seu.add.meta.from.table)
export(seu.map.and.add.new.ident.to.meta)
export(shorten_clustering_names)
export(showMiscSlots)
export(showToolsSlots)
export(sparse.cor)
export(suPlotVariableFeatures)
export(subsetSeuObjByIdent)
export(transferLabelsSeurat)
export(transferMetadata)
export(umapHiLightSel)
export(umapNamedClusters)
export(whitelist.subset.ls.Seurat)
export(writeCombinedMetadataToTsvFromLsObj)
export(ww.calc_helper)
export(ww.check.quantile.cutoff.and.clip.outliers)
export(ww.get.1st.Seur.element)
export(xread)
export(xsave)
import(Seurat)
import(tidyverse)
importFrom(CodeAndRoll2,as_tibble_from_namedVec)
importFrom(CodeAndRoll2,clip.outliers.at.percentile)
importFrom(CodeAndRoll2,df.col.2.named.vector)
importFrom(CodeAndRoll2,grepv)
importFrom(CodeAndRoll2,translate)
importFrom(EnhancedVolcano,EnhancedVolcano)
importFrom(HGNChelper,checkGeneSymbols)
importFrom(MarkdownHelpers,llogit)
importFrom(MarkdownHelpers,llprint)
importFrom(MarkdownHelpers,ww.assign_to_global)
importFrom(MarkdownReports,create_set_OutDir)
importFrom(MarkdownReports,create_set_SubDir)
importFrom(MarkdownReports,wbarplot)
importFrom(MarkdownReports,whist)
importFrom(MarkdownReports,wlegend)
importFrom(MarkdownReports,wplot)
importFrom(MarkdownReports,wplot_save_pheatmap)
importFrom(MarkdownReports,wplot_save_this)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,crossprod)
importFrom(Matrix,rowSums)
importFrom(Matrix,tcrossprod)
importFrom(R.utils,gunzip)
importFrom(R.utils,gzip)
importFrom(RColorBrewer,brewer.pal)
importFrom(ReadWriter,FirstCol2RowNames)
importFrom(ReadWriter,read.simple.tsv)
importFrom(Seurat,AddMetaData)
importFrom(Seurat,DimPlot)
importFrom(Seurat,DiscretePalette)
importFrom(Seurat,Embeddings)
importFrom(Seurat,FeaturePlot)
importFrom(Seurat,FeatureScatter)
importFrom(Seurat,FetchData)
importFrom(Seurat,FindAllMarkers)
importFrom(Seurat,FindClusters)
importFrom(Seurat,FindNeighbors)
importFrom(Seurat,FindTransferAnchors)
importFrom(Seurat,FindVariableFeatures)
importFrom(Seurat,GetAssayData)
importFrom(Seurat,NoAxes)
importFrom(Seurat,NoLegend)
importFrom(Seurat,Read10X)
importFrom(Seurat,RenameCells)
importFrom(Seurat,RunPCA)
importFrom(Seurat,RunTSNE)
importFrom(Seurat,RunUMAP)
importFrom(Seurat,ScaleData)
importFrom(Seurat,TransferData)
importFrom(Seurat,VariableFeatures)
importFrom(SeuratObject,UpdateSeuratObject)
importFrom(Stringendo,iprint)
importFrom(Stringendo,kollapse)
importFrom(Stringendo,kpp)
importFrom(Stringendo,kppu)
importFrom(Stringendo,percentage_formatter)
importFrom(checkmate,assert_character)
importFrom(checkmate,assert_class)
importFrom(checkmate,assert_string)
importFrom(cowplot,ggdraw)
importFrom(cowplot,ggsave2)
importFrom(cowplot,plot_grid)
importFrom(cowplot,save_plot)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,bind_rows)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,pull)
importFrom(dplyr,sample_n)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize)
importFrom(dplyr,summarize_all)
importFrom(dplyr,summarize_at)
importFrom(dplyr,top_n)
importFrom(foreach,"%dopar%")
importFrom(foreach,foreach)
importFrom(foreach,getDoParRegistered)
importFrom(fs,dir_ls)
importFrom(future,plan)
importFrom(ggExpress,qA4_grid_plot)
importFrom(ggExpress,qbarplot)
importFrom(ggExpress,qbarplot.df)
importFrom(ggExpress,qhistogram)
importFrom(ggExpress,qqSave)
importFrom(ggExpress,qscatter)
importFrom(ggExpress,qvenn)
importFrom(ggcorrplot,ggcorrplot)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,coord_polar)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_linedraw)
importFrom(ggplot2,theme_minimal)
importFrom(ggrepel,geom_text_repel)
importFrom(gplots,rich.colors)
importFrom(graphics,par)
importFrom(graphics,text)
importFrom(harmony,RunHarmony)
importFrom(htmlwidgets,saveWidget)
importFrom(matrixStats,rowSums2)
importFrom(pheatmap,pheatmap)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(princurve,principal_curve)
importFrom(princurve,whiskers)
importFrom(qs,qread)
importFrom(qs,qsave)
importFrom(readr,read_rds)
importFrom(readr,read_tsv)
importFrom(reshape2,melt)
importFrom(rstudioapi,isAvailable)
importFrom(scales,hue_pal)
importFrom(scales,percent)
importFrom(sparseMatrixStats,rowQuantiles)
importFrom(stats,cor)
importFrom(stats,cor.test)
importFrom(stats,sd)
importFrom(stringr,str_detect)
importFrom(stringr,str_split_fixed)
importFrom(tibble,deframe)
importFrom(tibble,rownames_to_column)
importFrom(tictoc,tic)
importFrom(tictoc,toc)
importFrom(tools,toTitleCase)