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All Projects → powellgenomicslab → Nebulosa

powellgenomicslab / Nebulosa

Licence: other
R package to visualize gene expression data based on weighted kernel density estimation

Programming Languages

r
7636 projects

Labels

single-cellsingle-cell-rna-seqsingle-cell-analysissingle-cell-multiomics

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Nebulosa

Build Status https://www.tidyverse.org/lifecycle/#maturing

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:

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")

Vignettes

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

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