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
Nebulosa can use
SingleCellExperiment objects. See the
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.