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

Bioconductor version: Release (3.18)

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 gmail.com>

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


To install this package, start R (version "4.3") and enter:

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


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 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 4.0), ggplot2, patchwork
Imports Seurat, SingleCellExperiment, SummarizedExperiment, ks, Matrix, stats, methods
System Requirements
URL https://github.com/powellgenomicslab/Nebulosa
Bug Reports https://github.com/powellgenomicslab/Nebulosa/issues
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, SeuratObject
Linking To
Depends On Me
Imports Me
Suggests Me scCustomize, SCpubr
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Nebulosa_1.12.0.tar.gz
Windows Binary Nebulosa_1.12.0.zip
macOS Binary (x86_64) Nebulosa_1.12.0.tgz
macOS Binary (arm64) Nebulosa_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Nebulosa
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Nebulosa
Bioc Package Browser https://code.bioconductor.org/browse/Nebulosa/
Package Short Url https://bioconductor.org/packages/Nebulosa/
Package Downloads Report Download Stats