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This is the development version of Nebulosa; for the stable release version, see Nebulosa.

Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation

Bioconductor version: Development (3.20)

This package provides a enhanced visualization of single-cell data based on gene-weighted density estimation. Nebulosa recovers the signal from dropped-out features and allows the inspection of the joint expression from multiple features (e.g. genes). Seurat and SingleCellExperiment objects can be used within Nebulosa.

Author: Jose Alquicira-Hernandez [aut, cre]

Maintainer: Jose Alquicira-Hernandez <alquicirajose at>

Citation (from within R, enter citation("Nebulosa")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Visualization of gene expression with Nebulosa HTML R Script
Visualization of gene expression with Nebulosa (in Seurat) HTML R Script
Reference Manual PDF


biocViews DimensionReduction, GeneExpression, SingleCell, Software, Visualization
Version 1.15.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 4.0), ggplot2, patchwork
Imports SingleCellExperiment, SummarizedExperiment, SeuratObject, ks, Matrix, stats, methods, ggrastr
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Suggests testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, Seurat
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Depends On Me
Imports Me
Suggests Me scCustomize, SCpubr
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Follow Installation instructions to use this package in your R session.

Source Package Nebulosa_1.15.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) Nebulosa_1.15.0.tgz
macOS Binary (arm64) Nebulosa_1.15.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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