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'))

Peer review:

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

Datasets:

On CRAN:

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

8.75 score 158 stars 237 scripts 706 downloads 34 exports 0 dependencies

Last updated 3 months agofrom:ebc5e868f5. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winNOTENov 19 2024
R-4.5-linuxNOTENov 19 2024
R-4.4-winNOTENov 19 2024
R-4.4-macNOTENov 19 2024
R-4.3-winNOTENov 19 2024
R-4.3-macNOTENov 19 2024

Exports:do_AffinityAnalysisPlotdo_AlluvialPlotdo_BarPlotdo_BeeSwarmPlotdo_BoxPlotdo_CellularStatesPlotdo_ChordDiagramPlotdo_ColorPalettedo_CopyNumberVariantPlotdo_CorrelationPlotdo_DimPlotdo_DotPlotdo_EnrichmentHeatmapdo_ExpressionHeatmapdo_FeaturePlotdo_GeyserPlotdo_GroupwiseDEPlotdo_LigandReceptorPlotdo_LoadingsPlotdo_MetadataPlotdo_NebulosaPlotdo_PathwayActivityPlotdo_RankedEnrichmentPlotdo_RankedExpressionPlotdo_RidgePlotdo_SCEnrichmentHeatmapdo_SCExpressionHeatmapdo_TermEnrichmentPlotdo_TFActivityPlotdo_ViolinPlotdo_VolcanoPlotdo_WafflePlotpackage_reportsave_Plot

Dependencies:

reference_manual

Rendered fromreference_manual.Rmdusingknitr::rmarkdownon Nov 19 2024.

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_AffinityAnalysisPlot
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
Generate color scales based on a value.do_ColorPalette
Display CNV scores from inferCNV as Feature Plots.do_CopyNumberVariantPlot
Create correlation matrix heatmaps.do_CorrelationPlot
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
Generate a Geyser plot.do_GeyserPlot
Compute a dotplot with the results of a group-wise DE analysis.do_GroupwiseDEPlot
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_LoadingsPlot
Compute a heatmap of categorical variables.do_MetadataPlot
Wrapper for Nebulosa::plot_density in Seurat.do_NebulosaPlot
Plot Pathway Activities from decoupleR using Progeny prior knowledge.do_PathwayActivityPlot
Compute a heatmap of enrichment of gene sets on the context of a diffusion component.do_RankedEnrichmentPlot
Compute a heatmap of enrichment of gene sets on the context of a diffusion component.do_RankedExpressionPlot
Create ridge plots.do_RidgePlot
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
Display the enriched terms for a given list of genes.do_TermEnrichmentPlot
Plot TF Activities from decoupleR using Dorothea prior knowledge.do_TFActivityPlot
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
Generate a status report of SCpubr and its dependencies.package_report
Save a plot as png, pdf and svg.save_Plot