Nebulosa

DOI: 10.18129/B9.bioc.Nebulosa  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

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

Details

biocViews	DimensionReduction, GeneExpression, SingleCell, Software, Visualization
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	GPL-3
Depends	R (>= 4.0), ggplot2, patchwork
Imports	Seurat, SingleCellExperiment, SummarizedExperiment, ks, Matrix, stats, methods
LinkingTo
Suggests	testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, SeuratObject
SystemRequirements
Enhances
URL	https://github.com/powellgenomicslab/Nebulosa
BugReports	https://github.com/powellgenomicslab/Nebulosa/issues
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_1.8.0.tar.gz
Windows Binary	Nebulosa_1.8.0.zip
macOS Binary (x86_64)	Nebulosa_1.8.0.tgz
macOS Binary (arm64)	Nebulosa_1.8.0.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