README.md

In powellgenomicslab/Nebulosa_Rv3: Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation

Nebulosa

Motivation

Due to the sparsity observed in single-cell data (e.g. RNA-seq, ATAC-seq), the visualization of cell features (e.g. gene, peak) is frequently affected and unclear, especially when it is overlaid with clustering to annotate cell types. Nebulosa is an R package to visualize data from single cells based on kernel density estimation. It aims to recover the signal from dropped-out features by incorporating the similarity between cells allowing a “convolution” of the cell features.

Installation

Nebulosa is available on Bioconductor and can be installed as follows (R >= 4.0):

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("Nebulosa")

See Nebulosa for more details.

You can install a temporary version of Nebulosa for (R < 4.0) from github via devtools:

devtools::install_github("powellgenomicslab/Nebulosa_Rv3")

Vignettes

Nebulosa can use Seurat and SingleCellExperiment objects. See the corresponding vignette:

• Seurat
• OSCA-Bioconductor

powellgenomicslab/Nebulosa_Rv3 documentation built on Sept. 18, 2020, 12:05 a.m.