Installation | Initial visualization | Merging with Dune | Initial ARI | Actual merging | ARI improvement | Session
Package: Dune 1.25.0
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_1.25.0.tar.gz
Dune_1.25.0.zip(r-4.7)Dune_1.25.0.zip(r-4.6)Dune_1.25.0.zip(r-4.5)
Dune_1.25.0.tgz(r-4.6-any)Dune_1.25.0.tgz(r-4.5-any)
Dune_1.25.0.tar.gz(r-4.7-any)Dune_1.25.0.tar.gz(r-4.6-any)
Dune_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Dune/json (API)
| # Install 'Dune' in R: |
| install.packages('Dune', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
On BioConductor:Dune-1.25.0(bioc 3.24)Dune-1.24.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
clusteringgeneexpressionrnaseqsoftwaresinglecelltranscriptomicsvisualization
Last updated from:fe1bd1f623. Checks:6 NOTE, 2 OK, 2 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 196 | ||
| linux-devel-x86_64 | NOTE | 435 | ||
| source / vignettes | OK | 264 | ||
| linux-release-x86_64 | NOTE | 416 | ||
| macos-release-arm64 | ERROR | 212 | ||
| macos-oldrel-arm64 | ERROR | 201 | ||
| windows-devel | NOTE | 314 | ||
| windows-release | NOTE | 319 | ||
| windows-oldrel | NOTE | 340 | ||
| wasm-release | OK | 196 |
Exports:ARIImpARIsARItrendclusterConversionConfusionEvolutionConfusionPlotDunefunctionTrackingintermediateMatNMIImpNMIsNMItrendplotARIsplotNMIsplotPrePostwhenToStop
Dependencies:abindaricodeBHBiobaseBiocGenericsBiocParallelclassclassIntclicodetoolscpp11crayonDBIDelayedArraydplyre1071farverformatRfutile.loggerfutile.optionsgenericsGenomicRangesgganimateggplot2gluegtablehmsIRangesisobandKernSmoothlabelinglambda.rlatticelifecyclelpSolvemagrittrMASSMatrixMatrixGenericsmatrixStatspillarpkgconfigprettyunitsprogressproxypurrrR6RColorBrewerRcpprlangs2S4ArraysS4VectorsS7scalesSeqinfosfsnowSparseArraystringistringrSummarizedExperimenttibbletidyrtidyselecttransformrtweenrunitsutf8vctrsviridisLitewithrwkXVector
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 |
