Package: Nebulosa 1.23.0

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:Jose Alquicira-Hernandez [aut, cre]

Nebulosa_1.23.0.tar.gz
Nebulosa_1.23.0.zip(r-4.7)Nebulosa_1.23.0.zip(r-4.6)Nebulosa_1.23.0.zip(r-4.5)
Nebulosa_1.23.0.tgz(r-4.6-any)Nebulosa_1.23.0.tgz(r-4.5-any)
Nebulosa_1.23.0.tar.gz(r-4.7-any)Nebulosa_1.23.0.tar.gz(r-4.6-any)
Nebulosa_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Nebulosa/json (API)

# Install 'Nebulosa' in R:
install.packages('Nebulosa', repos = c('https://bioc.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

10.18 score 115 stars 1 packages 808 scripts 3 mentions 1 exports 72 dependencies

Last updated from:3cd21b87ad. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE245
linux-devel-x86_64NOTE378
source / vignettesOK541
linux-release-x86_64NOTE364
macos-release-arm64NOTE182
macos-oldrel-arm64NOTE184
windows-develNOTE286
windows-releaseNOTE307
windows-oldrelNOTE258
wasm-releaseOK227

Exports:plot_density

Dependencies:abindbase64encbeeswarmBiobaseBiocGenericsCairoclicodetoolscpp11DelayedArraydigestdotCall64farverFNNfuturefuture.applygenericsGenomicRangesggbeeswarmggplot2ggrastrglobalsgluegtableIRangesisobandjsonlitekernlabKernSmoothkslabelinglatticelifecyclelistenvMatrixMatrixGenericsmatrixStatsmclustmgcvmulticoolmvtnormnlmeparallellypatchworkpngpracmaprogressrR6raggRColorBrewerRcppRcppEigenrlangS4ArraysS4VectorsS7scalesSeqinfoSeuratObjectSingleCellExperimentspspamSparseArraystringiSummarizedExperimentsystemfontstextshapingvctrsviporviridisLitewithrXVector

Visualization of gene expression with Nebulosa
Overview | Import libraries | Data pre-processing | Quality control | Data normalization | Dimensionality reduction | Clustering | Visualize data with Nebulosa | Multi-feature visualization | Identifying Naive CD8+ T cells | Identifying Naive CD4+ T cells | Conclusions
Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2020-10-08
Started: 2020-07-27

Visualization of gene expression with Nebulosa (in Seurat)
Overview | Import libraries | Data pre-processing | Data normalization | Dimensionality reduction | Clustering | Visualize data with Nebulosa | Multi-feature visualization | Identifying Naive CD8+ T cells | Identifying Naive CD4+ T cells | Conclusions
Rendered fromnebulosa_seurat.Rmdusingknitr::rmarkdown

Last update: 2020-08-18
Started: 2020-08-18

Readme and manuals

Help Manual

Help pageTopics
Estimate weighted kernel densitycalculate_density
Plot gene-weighted 2D kernel densityplot_density plot_density,Seurat-method plot_density,SingleCellExperiment-method
Plot density estimatesplot_density_
Weighted 2D kernel density estimationwkde2d