Nebulosa
This is the released version of Nebulosa; for the devel version, see Nebulosa.
Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, GeneExpression, SingleCell, Software, Visualization |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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_1.22.0.tar.gz |
| Windows Binary (x86_64) | Nebulosa_1.22.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | Nebulosa_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | Nebulosa_1.22.0.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 |