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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 (3.18)

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")):

Installation

To install this package, start R (version "4.3") 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 1.11.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License GPL-3
Depends R (>= 4.0), ggplot2, patchwork
Imports Seurat, SingleCellExperiment, SummarizedExperiment, ks, Matrix, stats, methods
Linking To
Suggests testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, SeuratObject
System Requirements
Enhances
URL https://github.com/powellgenomicslab/Nebulosa
Bug Reports https://github.com/powellgenomicslab/Nebulosa/issues
See More
Depends On Me
Imports Me
Suggests Me scCustomize, SCpubr
Links To Me
Build Report  

Package Archives

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

Source Package Nebulosa_1.11.0.tar.gz
Windows Binary Nebulosa_1.11.0.zip
macOS Binary (x86_64) Nebulosa_1.11.0.tgz
macOS Binary (arm64) Nebulosa_1.11.0.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