Package: Nebulosa 1.17.0
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_1.17.0.tar.gz
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Nebulosa_1.17.0.tgz(r-4.4-any)Nebulosa_1.17.0.tgz(r-4.3-any)
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Nebulosa_1.17.0.tgz(r-4.4-emscripten)
Nebulosa.pdf |Nebulosa.html✨
Nebulosa/json (API)
NEWS
| # 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-1.15.0(bioc 3.20)Nebulosa-1.14.0(bioc 3.19)
softwaregeneexpressionsinglecellvisualizationdimensionreductionsingle-cellsingle-cell-analysissingle-cell-multiomicssingle-cell-rna-seq
Last updated 23 days agofrom:29d69232bc. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 31 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
Exports:plot_density
Dependencies:abindaskpassbeeswarmBiobaseBiocGenericsCairoclicodetoolscolorspacecpp11crayoncurlDelayedArraydigestdotCall64fansifarverFNNfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrglobalsgluegtablehttrIRangesisobandjsonlitekernlabKernSmoothkslabelinglatticelifecyclelistenvmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmgcvmimemulticoolmunsellmvtnormnlmeopensslparallellypatchworkpillarpkgconfigpngpracmaprogressrR6raggRColorBrewerRcppRcppEigenrlangS4ArraysS4VectorsscalesSeuratObjectSingleCellExperimentspspamSparseArraySummarizedExperimentsyssystemfontstextshapingtibbleUCSC.utilsutf8vctrsviporviridisLitewithrXVectorzlibbioc
Visualization of gene expression with Nebulosa
Rendered fromintroduction.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2020-10-08
Started: 2020-07-27
Visualization of gene expression with Nebulosa (in Seurat)
Rendered fromnebulosa_seurat.Rmdusingknitr::rmarkdownon Oct 30 2024.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 |
