Package: bluster 1.15.1

Aaron Lun

bluster: Clustering Algorithms for Bioconductor

Wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results.

Authors:Aaron Lun [aut, cre], Stephanie Hicks [ctb], Basil Courbayre [ctb], Tuomas Borman [ctb], Leo Lahti [ctb]

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bluster.pdf |bluster.html
bluster/json (API)
NEWS

# Install 'bluster' in R:
install.packages('bluster', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:bluster-1.15.1(bioc 3.20)bluster-1.14.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologysoftwaregeneexpressiontranscriptomicssinglecellclustering

39 exports 9.36 score 25 dependencies 49 dependents 572 scripts 9.1k downloads

Last updated 1 months agofrom:32de7f0a3b. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 07 2024
R-4.5-win-x86_64NOTEOct 07 2024
R-4.5-linux-x86_64NOTEOct 07 2024
R-4.4-win-x86_64OKOct 07 2024
R-4.4-mac-x86_64OKOct 07 2024
R-4.4-mac-aarch64OKOct 07 2024
R-4.3-win-x86_64OKOct 07 2024
R-4.3-mac-x86_64OKOct 07 2024
R-4.3-mac-aarch64OKOct 07 2024

Exports:.defaultScalarArguments.extractScalarArguments.showScalarArgumentsAffinityParamAgnesParamapproxSilhouettebootstrapStabilitycenterscenters<-ClaraParamclusterRMSDclusterRowsclusterSweepcompareClusteringsDbscanParamDianaParamDmmParamHclustParamKmeansParamKNNGraphParamlinkClusterslinkClustersMatrixmakeKNNGraphmakeSNNGraphMbkmeansParammergeCommunitiesneighborPurityneighborsToKNNGraphneighborsToSNNGraphnestedClustersNNGraphParampairwiseModularitypairwiseRandPamParamshowSNNGraphParamSomParamTwoStepParamupdateObject

Dependencies:assortheadBHBiocGenericsBiocNeighborsBiocParallelcliclustercodetoolscpp11formatRfutile.loggerfutile.optionsglueigraphlambda.rlatticelifecyclemagrittrMatrixpkgconfigRcpprlangS4Vectorssnowvctrs

Flexible clustering for Bioconductor

Rendered fromclusterRows.Rmdusingknitr::rmarkdownon Oct 07 2024.

Last update: 2021-04-23
Started: 2020-07-19

Assorted clustering diagnostics

Rendered fromdiagnostics.Rmdusingknitr::rmarkdownon Oct 07 2024.

Last update: 2021-04-21
Started: 2020-07-19

Readme and manuals

Help Manual

Help pageTopics
Define the default arguments.defaultScalarArguments .defaultScalarArguments,BlusterParam-method .extractScalarArguments .showScalarArguments
Affinity propogationAffinityParam AffinityParam-class clusterRows,ANY,AffinityParam-method show,AffinityParam-method
Agglomerative nesting.defaultScalarArguments,AgnesParam-method AgnesParam AgnesParam-class clusterRows,ANY,AgnesParam-method show,AgnesParam-method
Approximate silhouette widthapproxSilhouette
The BlusterParam classBlusterParam-class show,BlusterParam-method [[,BlusterParam-method [[<-,BlusterParam-method
Assess cluster stability by bootstrappingbootstrapStability
Clustering Large Applications.defaultScalarArguments,ClaraParam-method ClaraParam ClaraParam-class clusterRows,ANY,ClaraParam-method show,ClaraParam-method
Compute the RMSD per clusterclusterRMSD
Cluster rows of a matrixclusterRows
Clustering parameter sweepsclusterSweep
Compare pairs of clusteringscompareClusterings
Density-based clustering with DBSCANclusterRows,ANY,DbscanParam-method DbscanParam DbscanParam-class show,DbscanParam-method
Divisive analysis clustering.defaultScalarArguments,DianaParam-method clusterRows,ANY,DianaParam-method DianaParam DianaParam-class show,DianaParam-method
Dirichlet multinomial mixture clusteringclusterRows,ANY,DmmParam-method DmmParam DmmParam-class show,DmmParam-method
The FixedNumberParam classcenters centers,FixedNumberParam-method centers<- centers<-,FixedNumberParam-method FixedNumberParam-class show,FixedNumberParam-method
Hierarchical clustering.defaultScalarArguments,HclustParam-method clusterRows,ANY,HclustParam-method HclustParam HclustParam-class show,HclustParam-method updateObject,HclustParam-method [[,HclustParam-method
The HierarchicalParam class.defaultScalarArguments,HierarchicalParam-method HierarchicalParam-class show,HierarchicalParam-method
K-means clusteringclusterRows,ANY,KmeansParam-method KmeansParam KmeansParam-class show,KmeansParam-method updateObject,KmeansParam-method
Create a graph between different clusteringslinkClusters linkClustersMatrix
Build a nearest-neighbor graphmakeKNNGraph makeSNNGraph neighborsToKNNGraph neighborsToSNNGraph
Mini-batch k-means clusteringclusterRows,ANY,MbkmeansParam-method MbkmeansParam MbkmeansParam-class show,MbkmeansParam-method
Merge communities from graph-based clusteringmergeCommunities
Compute neighborhood purityneighborPurity
Map nested clusteringsnestedClusters
Graph-based clusteringclusterRows,ANY,KNNGraphParam-method clusterRows,ANY,SNNGraphParam-method KNNGraphParam KNNGraphParam-class NNGraphParam NNGraphParam-class show,NNGraphParam-method SNNGraphParam SNNGraphParam-class
Compute pairwise modularitypairwiseModularity
Compute pairwise Rand indicespairwiseRand
Partitioning around medoids.defaultScalarArguments,PamParam-method clusterRows,ANY,PamParam-method PamParam PamParam-class show,PamParam-method
Clustering with self-organizing mapsclusterRows,ANY,SomParam-method show,SomParam-method SomParam SomParam-class
Two step clustering with vector quantizationclusterRows,ANY,TwoStepParam-method show,TwoStepParam-method TwoStepParam TwoStepParam-class