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 (3.22)
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]
Maintainer: Jose Alquicira-Hernandez <alquicirajose at gmail.com>
citation("Nebulosa")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, GeneExpression, SingleCell, Software, Visualization |
| Version | 1.19.0 |
| 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 |
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_1.19.0.tar.gz |
| Windows Binary (x86_64) | Nebulosa_1.19.0.zip |
| macOS Binary (x86_64) | Nebulosa_1.19.0.tgz |
| macOS Binary (arm64) | Nebulosa_1.19.0.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 |