Nebulosa

This is the released version of Nebulosa; for the devel version, see Nebulosa.

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

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.Nebulosa

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0002-9049-7780

Maintainer: Jose Alquicira-Hernandez <alquicirajose at gmail.com>

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

Installation

To install this package, start R (version "4.5") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DimensionReduction, GeneExpression, SingleCell, Software, Visualization

Version 1.20.0

In Bioconductor since BioC 3.12 (R-4.0) (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

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_1.20.0.tar.gz

Windows Binary (x86_64) Nebulosa_1.19.0.zip

macOS Binary (x86_64) Nebulosa_1.20.0.tgz

macOS Binary (arm64) Nebulosa_1.20.0.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