Package: immunoClust 1.37.3

Till Soerensen

immunoClust: immunoClust - Automated Pipeline for Population Detection in Flow Cytometry

immunoClust is a model based clustering approach for Flow Cytometry samples. The cell-events of single Flow Cytometry samples are modelled by a mixture of multinominal normal- or t-distributions. The cell-event clusters of several samples are modelled by a mixture of multinominal normal-distributions aiming stable co-clusters across these samples.

Authors:Till Soerensen [aut, cre]

immunoClust_1.37.3.tar.gz
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immunoClust.pdf |immunoClust.html✨
immunoClust/json (API)
NEWS

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

Peer review:

Uses libs:
  • gsl– GNU Scientific Library (GSL)
  • c++– GNU Standard C++ Library v3
Datasets:
  • dat.exp - ImmunoClust Meta-clustering Sample
  • dat.fcs - ImmunoClust Cell-clustering Sample
  • dat.meta - ImmunoClust Meta-clustering Results Sample

On BioConductor:immunoClust-1.37.3(bioc 3.20)immunoClust-1.36.0(bioc 3.19)

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

bioconductor-package

87 exports 1.31 score 12 dependencies 2 mentions

Last updated 1 months agofrom:e781cfaa26

Exports:addLevel<-aposterioribhattacharyya.coeffbhattacharyya.distbhattacharyya.probcell.Classifycell.classifyAllcell.ClustDatacell.EMcell.EMstepcell.EMtcell.Estepcell.Estimationcell.FitModelcell.hclustcell.InitialModelcell.MajorIterationLoopcell.MajorIterationTranscell.MEcell.MEstepcell.Mstepcell.processcell.SubClusteringcell.TestSubClustercellsclassifiedclusterCoeffclusterDistclusterProbclustersdescdesc<-descFulleventsfinalizefindLevelimmunoMetalabellevellevel<-meta.Clusteringmeta.exprsmeta.freqTablemeta.hclustmeta.MEmeta.Normalizemeta.numClustersmeta.numEventsmeta.parMFImeta.processmeta.RegNormmeta.relEventsmeta.relParentmeta.SON.clusteringmeta.SON.combineClusteringmeta.SubClusteringmeta.TestSubClustermove<-munclsnobsnparnsamparametersparent<-plotpropprop<-remove<-removed.aboveremoved.belowsam_clsEventssam_clsMusam_clsSigmasam_clsWeightssam_nclsshowsigmasplomsubsetsummarytrans.ApplyToDatatrans.FitToDatatransfer<-transformParamsunclassifiedweights

Dependencies:BHBiobaseBiocGenericscpp11cytolibflowCorelatticematrixStatsRcppRhdf5libRProtoBufLibS4Vectors

immunoClust package

Rendered fromimmunoClust.Rnwusingutils::Sweaveon Jun 28 2024.

Last update: 2022-12-08
Started: 2015-03-13

Readme and manuals

Help Manual

Help pageTopics
immunoClust - Automated Pipeline for Population Detection in Flow CytometryimmunoClust-package immunoClust immunoClust.package
Bhattacharyya Distance, Coefficient and Probabilitybhattacharyya.coeff bhattacharyya.dist bhattacharyya.prob
Model Based Clustering of Data for a pre-defined Number of Clusterscell.ClustData
immunoClust EMt-iteration on Cell-events given initial Model Parameterscell.EM cell.EMstep cell.EMt cell.Estep cell.Estimation
immunoClust EMt-iteration on Cell-events given initial Model Parameterscell.Classify cell.FitModel
Hierarchical Model Based Clustering of Cell-events in the immunoClust-pipelinecell.hclust
immunoClust EM-iteration on Cell-events given initial Cluster Membership Assignmentcell.ME cell.MEstep cell.Mstep
Clustering of Cell-events in the immunoClust-pipelinecell.classifyAll cell.InitialModel cell.MajorIterationLoop cell.MajorIterationTrans cell.process
Brief Information of removed Cell-events by immunoClust Cell-event Clusteringremoved.above removed.below
immunoClust Model Refinement Step in iterative Cell-events Clusteringcell.SubClustering cell.TestSubCluster
immunoClust Meta-clustering Sampledat.exp
immunoClust Cell-clustering Sampledat.fcs
immunoClust Meta-clustering Results Sampledat.meta
Generic function definitions in immunoClustaposteriori clusterCoeff clusterDist clusterProb label mu ncls nobs npar nsam parameters parameters<- sam_clsEvents sam_clsMu sam_clsSigma sam_clsWeights sam_ncls sigma subset transformParams weights
immunoClust-ObjectimmunoClust-class immunoClust.object show show,immunoClust-method show.immunoClust summary summary,immunoClust-method summary.immunoClust
'immunoMeta': a class for storing meta-clustering resultsimmunoMeta immunoMeta-class immunoMeta-object immunoMeta.class immunoMeta.object show,immunoMeta-method show.immunoMeta summary,immunoMeta-method summary.immunoMeta
Clustering of Cell-clusters in the immunoClust-pipelinemeta.Clustering
immunoClust Meta-clustering Results Exportmeta.export meta.freqTable meta.majorEvents meta.numClusters meta.numEvents meta.parMFI meta.relEvents meta.relEvents2 meta.relEvents3 meta.relParent
Collecting Data of an immunoClust vectormeta.exprs
Hierarchical Meta-clustering of Cell-clusters in the immunoClust-pipelinemeta.hclust
immunoClust EM(t)-iteration on Cell-clustersmeta.ME
immunoClust normalization step with the meta.clustering processmeta.Normalize
Meta-clustering of Cell-clusters in the immunoClust-pipelinemeta.process
immunoClust normalization proceduremeta.RegNorm
meta clustering process with internal SON normalisationmeta.SON.clustering
Transfer the annotation of an immunoMeta-object to an immunoClust-object.meta.SON.combineClustering
immunoClust Model Refinement Step in iterative Meta-clusteringmeta.SubClustering meta.TestSubCluster
Acessors and Methods for immunoClust Objectsaposteriori,immunoClust-method aposteriori.immunoClust cells cells,immunoClust-method events,immunoClust-method events.immunoClust label,immunoClust-method label.immunoClust mu,immunoClust-method mu.immunoClust ncls,immunoClust-method ncls.immunoClust nobs,immunoClust-method nobs.immunoClust npar,immunoClust-method npar.immunoClust parameters,immunoClust-method parameters.immunoClust parameters<-,immunoClust,character-method parameters<-.immunoClust sigma,immunoClust-method sigma.immunoClust subset,immunoClust-method subset.immunoClust transformParams,immunoClust-method transformParams.immunoClust weights,immunoClust-method weights.immunoClust
Acessors and Methods for immunoMeta ObjectsaddLevel<- addLevel<-.immunoMeta aposteriori,immunoMeta-method aposteriori.immunoMeta classified classified,immunoMeta-method classified.immunoMeta clusterCoeff,immunoMeta-method clusterDist,immunoMeta-method clusterProb,immunoMeta-method clusters clusters,immunoMeta-method clusters.immunoMeta desc desc,immunoMeta-method desc.immunoMeta desc<- desc<-,immunoMeta-method desc<-.immunoMeta descFull descFull,immunoMeta-method descFull.immunoMeta events events,immunoMeta-method events.immunoMeta finalize finalize,immunoMeta-method finalize.immunoMeta findLevel findLevel,immunoMeta-method findLevel.immunoMeta label,immunoMeta-method label.immunoMeta level level,immunoMeta-method level.immunoMeta level<- level<-.immunoMeta move<- move<-.immunoMeta mu,immunoMeta-method mu.immunoMeta ncls,immunoMeta-method ncls.immunoMeta nobs,immunoMeta-method nobs.immunoMeta npar,immunoMeta-method npar.immunoMeta nsam,immunoMeta-method nsam.immunoMeta parameters,immunoMeta-method parameters.immunoMeta parameters<-,immunoMeta,character-method parameters<-.immunoMeta parent<- parent<-.immunoMeta parent<-.immunoMeta-method prop prop,immunoMeta-method prop.immunoMeta prop<- prop<-,immunoMeta-method prop<-.immunoMeta remove<- remove<-.immunoMeta sam_clsEvents,immunoMeta-method sam_clsEvents.immunoMeta sam_clsMu,immunoMeta-method sam_clsMu.immunoMeta sam_clsSigma,immunoMeta-method sam_clsSigma.immunoMeta sam_clsWeights,immunoMeta-method sam_clsWeights.immunoMeta sam_ncls,immunoMeta-method sam_ncls.immunoMeta sigma,immunoMeta-method sigma.immunoMeta subset,immunoMeta-method subset.immunoMeta transfer<- transfer<-,immunoMeta,immunoMeta-method transfer<-.immunoMeta transformParams,immunoMeta-method transformParams.immunoMeta unclassified unclassified,immunoMeta-method unclassified.immunoMeta weights,immunoMeta-method weights.immunoMeta
Scatterplot of immunoClust Clustering Resultsplot,immunoClust,missing-method plot,immunoClust-method plot.immunoClust
Scatterplot of immunoMeta Structured Clustering Resultsplot,immunoMeta,missing-method plot,immunoMeta-method plot.immunoMeta
Scatterplot Matrix of immunoClust Clustering ResultsdatSplom splom splom,immunoClust,flowFrame-method splom,immunoClust,matrix-method splom,immunoClust,missing-method splom.immunoClust
immunoClust asinh-Transformationtrans.ApplyToData
immunoClust asinh-Transformation Optimizationtrans.FitToData