Package: SCpubr 2.0.2.9000

SCpubr: Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

A system that provides a streamlined way of generating publication ready plots for known Single-Cell transcriptomics data in a “publication ready” format. This is, the goal is to automatically generate plots with the highest quality possible, that can be used right away or with minimal modifications for a research article.

Authors:Enrique Blanco-Carmona [cre, aut]

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SCpubr.pdf |SCpubr.html✨
SCpubr/json (API)
NEWS

# Install 'SCpubr' in R:
install.packages('SCpubr', repos = c('https://enblacar.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/enblacar/scpubr/issues

Datasets:

On CRAN:

Conda:

softwaresinglecellvisualizationdata-visualizationggplot2publication-quality-plotsseuratsingle-cellsingle-cell-genomicssingle-cell-rna-seq

8.71 score 178 stars 194 scripts 773 downloads 35 exports 0 dependencies

Last updated 1 months agofrom:1eb179b28f. Checks:1 OK, 8 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 15 2025
R-4.5-winWARNINGMar 15 2025
R-4.5-macWARNINGMar 15 2025
R-4.5-linuxWARNINGMar 15 2025
R-4.4-winWARNINGMar 15 2025
R-4.4-macWARNINGMar 15 2025
R-4.4-linuxWARNINGMar 15 2025
R-4.3-winWARNINGMar 15 2025
R-4.3-macWARNINGMar 15 2025

Exports:do_ActivityHeatmapdo_AlluvialPlotdo_BarPlotdo_BeeSwarmPlotdo_BoxPlotdo_CellularStatesPlotdo_ChordDiagramPlotdo_CNVHeatmapdo_ColorBlindCheckdo_ColorPalettedo_CorrelationHeatmapdo_DimPlotdo_DotPlotdo_EnrichmentHeatmapdo_ExpressionHeatmapdo_FeaturePlotdo_GroupwiseDEHeatmapdo_LigandReceptorPlotdo_LoadingsHeatmapdo_MetadataHeatmapdo_NebulosaPlotdo_PackageReportdo_PathwayActivityHeatmapdo_RankedEnrichmentHeatmapdo_RankedExpressionHeatmapdo_RidgePlotdo_SavePlotdo_SCEnrichmentHeatmapdo_SCExpressionHeatmapdo_StripPlotdo_TermEnrichmentPlotdo_TFActivityHeatmapdo_ViolinPlotdo_VolcanoPlotdo_WafflePlot

Dependencies:

reference_manual

Rendered fromreference_manual.Rmdusingknitr::rmarkdownon Mar 15 2025.

Last update: 2023-07-31
Started: 2022-10-10

Readme and manuals

Help Manual

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