Package: Nebulosa 1.22.0
Jose Alquicira-Hernandez
Nebulosa: Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation
This package provides a enhanced visualization of single-cell data based on gene-weighted density estimation. Nebulosa recovers the signal from dropped-out features and allows the inspection of the joint expression from multiple features (e.g. genes). Seurat and SingleCellExperiment objects can be used within Nebulosa.
Authors:
Nebulosa_1.22.0.tar.gz
Nebulosa_1.22.0.zip(r-4.7)Nebulosa_1.22.0.zip(r-4.6)Nebulosa_1.22.0.zip(r-4.5)
Nebulosa_1.22.0.tgz(r-4.6-any)Nebulosa_1.22.0.tgz(r-4.5-any)
Nebulosa_1.22.0.tar.gz(r-4.7-any)Nebulosa_1.22.0.tar.gz(r-4.6-any)
Nebulosa_1.22.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Nebulosa/json (API)
NEWS
| # Install 'Nebulosa' in R: |
| install.packages('Nebulosa', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/powellgenomicslab/nebulosa/issues
On BioConductor:Nebulosa-1.23.0(bioc 3.24)Nebulosa-1.22.0(bioc 3.23)
softwaregeneexpressionsinglecellvisualizationdimensionreductionsingle-cellsingle-cell-analysissingle-cell-multiomicssingle-cell-rna-seq
Last updated from:c496ec9d84 (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 230 | ||
| linux-devel-x86_64 | NOTE | 402 | ||
| source / vignettes | OK | 550 | ||
| linux-release-x86_64 | NOTE | 406 | ||
| macos-release-arm64 | NOTE | 198 | ||
| macos-oldrel-arm64 | NOTE | 195 | ||
| windows-devel | NOTE | 270 | ||
| windows-release | NOTE | 295 | ||
| windows-oldrel | NOTE | 295 | ||
| wasm-release | OK | 193 |
Exports:plot_density
Dependencies:abindbase64encbeeswarmBiobaseBiocGenericsCairoclicodetoolscpp11DelayedArraydigestdotCall64farverFNNfuturefuture.applygenericsGenomicRangesggbeeswarmggplot2ggrastrglobalsgluegtableIRangesisobandjsonlitekernlabKernSmoothkslabelinglatticelifecyclelistenvMatrixMatrixGenericsmatrixStatsmclustmgcvmulticoolmvtnormnlmeparallellypatchworkpngpracmaprogressrR6raggRColorBrewerRcppRcppEigenrlangS4ArraysS4VectorsS7scalesSeqinfoSeuratObjectSingleCellExperimentspspamSparseArraystringiSummarizedExperimentsystemfontstextshapingvctrsviporviridisLitewithrXVector
Visualization of gene expression with Nebulosa
Rendered fromintroduction.Rmdusingknitr::rmarkdownon Jun 07 2026.Last update: 2020-10-08
Started: 2020-07-27
Visualization of gene expression with Nebulosa (in Seurat)
Rendered fromnebulosa_seurat.Rmdusingknitr::rmarkdownon Jun 07 2026.Last update: 2020-08-18
Started: 2020-08-18
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Estimate weighted kernel density | calculate_density |
| Plot gene-weighted 2D kernel density | plot_density plot_density,Seurat-method plot_density,SingleCellExperiment-method |
| Plot density estimates | plot_density_ |
| Weighted 2D kernel density estimation | wkde2d |
