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.

Nebulosa is available on Bioconductor and can be installed as follows:

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

BiocManager::install("Nebulosa")

See Nebulosa for more details.

You can install the developing version of Nebulosa from github via devtools:

devtools::install_github("powellgenomicslab/Nebulosa")

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

• Seurat
• OSCA-Bioconductor