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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(addAttributeToGraph)
export(addCellNamesToGraph)
export(calcNhoodSim)
export(computePseudocells)
export(downsampleSCE)
export(exportToGMT)
export(filterSharedFeatures)
export(getCelltypeColours)
export(getDiscreteColours)
export(getEnsemblHomologs)
export(getGenesFromGOTerms)
export(getMaxMappings)
export(getMeanExpression)
export(getNhoodPositions)
export(getSharedUniqueMarkers)
export(getStageColours)
export(loadRabbitData)
export(loadReadsAroundGRange)
export(loadTyser2020)
export(loadWOTData)
export(loadYang2021)
export(plotAnnotatedUMAP)
export(plotAnnotationAlluvium)
export(plotGeneUMAP)
export(plotNhoodMappings)
export(plotNhoodMaxSim)
export(plotNhoodSimGroups)
export(plotNhoodSizeHist)
export(plotPseudocells)
export(plotReadDistsNearGene)
export(plotTrajMappings)
export(prepareEdgeR)
export(runEdgeR)
export(subsetMiloGraph)
export(subsetMiloGroups)
importFrom(DelayedArray,rowMeans)
importFrom(IRanges,distanceToNearest)
importFrom(Matrix,Diagonal)
importFrom(Matrix,Matrix)
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,colData)
importFrom(SingleCellExperiment,reducedDim)
importFrom(biomaRt,getBM)
importFrom(biomaRt,useMart)
importFrom(data.table,data.table)
importFrom(data.table,setnames)
importFrom(dplyr,"%>%")
importFrom(edgeR,estimateDisp)
importFrom(edgeR,glmQLFTest)
importFrom(edgeR,glmQLFit)
importFrom(edgeR,topTags)
importFrom(ggalluvial,geom_alluvium)
importFrom(ggalluvial,geom_flow)
importFrom(ggalluvial,geom_stratum)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guides)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggraph,create_layout)
importFrom(ggraph,geom_edge_link0)
importFrom(ggraph,geom_node_point)
importFrom(ggraph,get_edges)
importFrom(ggraph,ggraph)
importFrom(ggrastr,rasterise)
importFrom(ggrepel,geom_text_repel)
importFrom(ggridges,geom_density_ridges)
importFrom(ggridges,theme_ridges)
importFrom(igraph,V)
importFrom(igraph,induced_subgraph)
importFrom(igraph,simplify)
importFrom(igraph,vertex_attr)
importFrom(miloR,nhoodGraph)
importFrom(scater,logNormCounts)
importFrom(stats,aggregate)
importFrom(viridis,scale_color_viridis)
importFrom(viridis,scale_colour_viridis)