Package: Dune 1.19.0
Hector Roux de Bezieux
Dune: Improving replicability in single-cell RNA-Seq cell type discovery
Given a set of clustering labels, Dune merges pairs of clusters to increase mean ARI between labels, improving replicability.
Authors:
Dune_1.19.0.tar.gz
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Dune.pdf |Dune.html✨
Dune/json (API)
NEWS
| # Install 'Dune' in R: |
| install.packages('Dune', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:Dune-1.17.0(bioc 3.20)Dune-1.16.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
clusteringgeneexpressionrnaseqsoftwaresinglecelltranscriptomicsvisualization
Last updated 23 days agofrom:4205bcf9c8. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | ERROR | Oct 30 2024 |
| R-4.3-win | NOTE | Oct 30 2024 |
| R-4.3-mac | ERROR | Oct 30 2024 |
Exports:ARIImpARIsARItrendclusterConversionConfusionEvolutionConfusionPlotDunefunctionTrackingintermediateMatNMIImpNMIsNMItrendplotARIsplotNMIsplotPrePostwhenToStop
Dependencies:abindaricodeaskpassBHBiobaseBiocGenericsBiocParallelclassclassIntclicodetoolscolorspacecpp11crayoncurlDBIDelayedArraydplyre1071fansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgganimateggplot2gluegtablehmshttrIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelpSolvemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigprettyunitsprogressproxypurrrR6RColorBrewerRcpprlangs2S4ArraysS4VectorsscalessfsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttransformrtweenrUCSC.utilsunitsutf8vctrsviridisLitewithrwkXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| adjustedRandIndex | .adjustedRandIndex |
| ARI improvement | ARIImp |
| ARI Matrix | ARIs |
| ARI improvement plot | ARItrend |
| A clustering matrix used to demonstrate the ari-merging process. | clusMat |
| clusterConversion | clusterConversion |
| Plot the evolution of the ConfusionPlot as merging happens | ConfusionEvolution |
| Plot confusion matrix | ConfusionPlot |
| Dune | Dune Dune,data.frame-method Dune,matrix-method Dune,SummarizedExperiment-method |
| Track the evolution of a function along merging | functionTracking |
| Find the clustering matrix that we would get if we stopped the ARI merging early | intermediateMat |
| NMI improvement | NMIImp |
| NMI Matrix | NMIs |
| NMI improvement plot | NMItrend |
| Cluster labels for a subset of the allen Smart-Seq nuclei dataset | nuclei |
| Plot an heatmap of the ARI matrix | plotARIs |
| Plot an heatmap of the NMI matrix | plotNMIs |
| Plot the reduction in cluster size for an ARI merging with 'Dune' | plotPrePost |
| When to Stop | whenToStop |
