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Nebulosa

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 (3.19)

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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("Nebulosa")

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

Documentation

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

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

Details

biocViews DimensionReduction, GeneExpression, SingleCell, Software, Visualization
Version 1.13.1
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
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, Seurat
Linking To
Enhances
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_1.13.1.tar.gz
Windows Binary Nebulosa_1.13.1.zip (64-bit only)
macOS Binary (x86_64) Nebulosa_1.13.1.tgz
macOS Binary (arm64) Nebulosa_1.13.1.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