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Bioconductor - Nebulosa (development version)

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] 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")

# 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 PDF NEWS Text Details biocViews DimensionReduction, GeneExpression, SingleCell, Software, Visualization Version 1.19.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 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.

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