Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

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Documentation for package ‘SCpubr’ version 3.0.0

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

Help Pages

do_ActivityHeatmap	Compute affinity of gene sets to cell populations using decoupleR.
do_AlluvialPlot	Generate Alluvial plots.
do_BarPlot	Create Bar Plots.
do_BeeSwarmPlot	BeeSwarm plot.
do_BoxPlot	Generate Box Plots.
do_CellularStatesPlot	Cellular States plot.
do_ChordDiagramPlot	Generate a Chord diagram.
do_CNVHeatmap	Display CNV scores from inferCNV as Feature Plots.
do_ColorBlindCheck	Generate colorblind variations of a given color palette.
do_ColorPalette	Generate color scales based on a value.
do_CorrelationHeatmap	Create correlation matrix heatmaps.
do_DimPlot	Wrapper for DimPlot.
do_DotPlot	This function is a wrapper for DotPlot. It provides most of its functionalities while adding extra. You can
do_EnrichmentHeatmap	Create enrichment scores heatmaps.
do_ExpressionHeatmap	Create heatmaps of averaged expression by groups.
do_FeaturePlot	Wrapper for FeaturePlot.
do_GroupwiseDEHeatmap	Compute a dotplot with the results of a group-wise DE analysis.
do_LigandReceptorPlot	Visualize Ligand-Receptor analysis output.
do_LoadingsHeatmap	Compute a heatmap summary of the top and bottom genes in the PCA loadings for the desired PCs in a Seurat object.
do_MetadataHeatmap	Compute a heatmap of categorical variables.
do_NebulosaPlot	Wrapper for Nebulosa::plot_density in Seurat.
do_PackageReport	Generate a status report of SCpubr and its dependencies.
do_PathwayActivityHeatmap	Plot Pathway Activities from decoupleR using Progeny prior knowledge.
do_RankedEnrichmentHeatmap	Compute a heatmap of enrichment of gene sets on the context of a dimensional reduction component.
do_RankedExpressionHeatmap	Compute a heatmap of expression of genes on the context of a dimensional reduction component.
do_RidgePlot	Create ridge plots.
do_SCEnrichmentHeatmap	Perform a single-cell-based heatmap showing the enrichment in a list of gene sets.
do_SCExpressionHeatmap	Perform a single-cell-based heatmap showing the expression of genes.
do_StripPlot	Generate a Strip plot.
do_TermEnrichmentPlot	Display the enriched terms for a given list of genes.
do_TFActivityHeatmap	Plot TF Activities from decoupleR using Dorothea prior knowledge.
do_ViolinPlot	Wrapper for VlnPlot.
do_VolcanoPlot	Compute a Volcano plot out of DE genes.
do_WafflePlot	Display the enriched terms for a given list of genes.
human_chr_locations	Chromosome arm locations for human genome GRCh38.