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 (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
Nebulosa can use
SingleCellExperiment objects. See the
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