Package index
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volcano_plot() - Volcano plot of differential-expression results
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clean_volcano_data() - Prepare a table for volcano plotting
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colour_volcano_points() - Per-point colours for a volcano plot
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alpha_volcano_points() - Per-point alpha for a volcano plot
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size_volcano_points() - Per-point size for a volcano plot
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basic_heatmap() - Basic clustered heatmap
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dendrogram_samples() - Sample dendrogram
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plot_correlation() - Plot a correlation ranking
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sc_correlation() - Gene-gene correlation across single cells
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correlation_heatmaps() - Heatmaps of top correlated genes
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umap_optimise() - Optimise UMAP hyper-parameters for a Seurat object
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go_enrichment() - Gene Ontology over-representation analysis
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convert_mouse_to_human()convert_human_to_mouse() - Convert gene symbols between mouse and human
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tcga_survival() - Overall-survival analysis of a TCGA cohort
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download_tcga_rnaseq() - Download a TCGA RNA-seq dataset
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stratify_by_expression() - Split samples into high and low expressers of a gene or signature
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make_transparent() - Make a colour transparent
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get_batlow() - Batlow colour palette
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moving_average() - Moving average of a numeric vector
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standardize() - Row-wise robust standardisation
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custom_enhanced_volcano() - Enhanced volcano plot (deprecated wrapper)
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makeTransparent()Get.batlow()calc.moving.average()basic.heatmap()dendrogram()convert.mouse.to.human()convert.human.to.mouse()GO.function()UMAP.optimise()clean.data.volcano()colour.points.volcano()alpha.points.volcano()size.points.volcano()custom.enhanced.volcano()sc.correlation()correlation.heatmaps()download.TCGA.RNAseq()TCGA.OS() - Deprecated dot.case function names