Nebulosa

DOI: 10.18129/B9.bioc.Nebulosa    

This is the development version of Nebulosa; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.12)

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 "4.0") and enter:

if (!requireNamespace("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")

 

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 0.99.94
In Bioconductor since BioC 3.12 (R-4.0)
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
SystemRequirements
Enhances
URL https://github.com/powellgenomicslab/Nebulosa
BugReports https://github.com/powellgenomicslab/Nebulosa/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package Nebulosa_0.99.94.tar.gz
Windows Binary Nebulosa_0.99.94.zip
macOS 10.13 (High Sierra) Nebulosa_0.99.94.tgz
Source Repository git clone https://git.bioconductor.org/packages/Nebulosa
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Nebulosa
Package Short Url https://bioconductor.org/packages/Nebulosa/
Package Downloads Report Download Stats

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