Package: immunoClust 1.45.0

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]

# Install 'immunoClust' in R:

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

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-1.45.0(bioc 3.24)immunoClust-1.44.0(bioc 3.23)

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

clustering flowcytometry singlecell cellbasedassays immunooncology gsl cpp

3.78 score 6 scripts 494 downloads 2 mentions 85 exports 16 dependencies

Last updated from:0c88cb519a. Checks:1 WARNING, 13 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	174
linux-devel-arm64	OK	262
linux-devel-x86_64	OK	287
source / vignettes	OK	398
linux-release-arm64	OK	240
linux-release-x86_64	OK	345
macos-release-arm64	OK	180
macos-release-x86_64	OK	366
macos-oldrel-arm64	OK	184
macos-oldrel-x86_64	OK	328
windows-devel	OK	284
windows-release	OK	288
windows-oldrel	OK	292
wasm-release	OK	138

Exports:addLevel<-aposteriori bhattacharyya.coeff bhattacharyya.dist bhattacharyya.prob cell.Classify cell.classifyAll cell.ClustData cell.EMstep cell.EMt cell.Estep cell.FitModel cell.hclust cell.InitialModel cell.MajorIterationLoop cell.MajorIterationTrans cell.MEstep cell.Mstep cell.process cell.SubClustering cell.TestSubCluster cells classified clusterCoeff clusterDist clusterProb clusters desc desc<-descFull events finalize findLevel immunoMeta label level level<-meta.Clustering meta.exprs meta.freqTable meta.hclust meta.ME meta.Normalize meta.numClusters meta.numEvents meta.parMFI meta.process meta.RegNorm meta.relEvents meta.relParent meta.SON.clustering meta.SON.combineClustering meta.SubClustering meta.TestSubCluster move<-mu ncls nobs npar nsam parameters parent<-plot prop prop<-remove<-removed.above removed.below sam_clsEvents sam_clsMu sam_clsSigma sam_clsWeights sam_names sam_ncls show sigma splom subset summary trans.ApplyToData trans.FitToData transfer<-transformParams unclassified weights

Dependencies:BH Biobase BiocGenerics biocmake cpp11 cytolib dir.expiry filelock flowCore generics lattice matrixStats Rcpp Rhdf5lib RProtoBufLib S4Vectors

immunoClust package

1 Licensing | 2 Overview | 3 Getting started | 4 Example Illustrating the immunoClust Pipeline | 5 Session Info

Rendered fromimmunoClust.Rnwusingutils::Sweave

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
immunoClust - Automated Pipeline for Population Detection in Flow Cytometry	immunoClust-package immunoClust immunoClust.package
Bhattacharyya Distance, Coefficient and Probability	bhattacharyya.coeff bhattacharyya.dist bhattacharyya.prob
Model Based Clustering of Data for a pre-defined Number of Clusters	cell.ClustData
immunoClust EMt-iteration on Cell-events given initial Model Parameters	cell.EMstep cell.EMt cell.Estep
immunoClust EMt-iteration on Cell-events given initial Model Parameters	cell.Classify cell.FitModel
Hierarchical Model Based Clustering of Cell-events in the immunoClust-pipeline	cell.hclust
immunoClust EM-iteration on Cell-events given initial Cluster Membership Assignment	cell.MEstep cell.Mstep
Clustering of Cell-events in the immunoClust-pipeline	cell.classifyAll cell.InitialModel cell.MajorIterationLoop cell.MajorIterationTrans cell.process
Brief Information of removed Cell-events by immunoClust Cell-event Clustering	removed.above removed.below
immunoClust Model Refinement Step in iterative Cell-events Clustering	cell.SubClustering cell.TestSubCluster
immunoClust Meta-clustering Sample	dat.exp
immunoClust Cell-clustering Sample	dat.fcs
immunoClust Meta-clustering Results Sample	dat.meta
Generic function definitions in immunoClust	aposteriori clusterCoeff clusterDist clusterProb label mu ncls nobs npar nsam parameters parameters<- sam_clsEvents sam_clsMu sam_clsSigma sam_clsWeights sam_names sam_ncls sigma subset transformParams weights
immunoClust-Object	immunoClust-class immunoClust.object show show,immunoClust-method show.immunoClust summary summary,immunoClust-method summary.immunoClust
'immunoMeta': a class for storing meta-clustering results	immunoMeta 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-pipeline	meta.Clustering
immunoClust Meta-clustering Results Export	meta.export meta.freqTable meta.majorEvents meta.numClusters meta.numEvents meta.parMFI meta.relEvents meta.relEvents2 meta.relEvents3 meta.relParent
Collecting Data of an immunoClust vector	meta.exprs
Hierarchical Meta-clustering of Cell-clusters in the immunoClust-pipeline	meta.hclust
immunoClust EM(t)-iteration on Cell-clusters	meta.ME
immunoClust normalization step with the meta.clustering process	meta.Normalize
Meta-clustering of Cell-clusters in the immunoClust-pipeline	meta.process
immunoClust normalization procedure	meta.RegNorm
meta clustering process with internal SON normalisation	meta.SON.clustering
Transfer the annotation of an immunoMeta-object to an immunoClust-object.	meta.SON.combineClustering
immunoClust Model Refinement Step in iterative Meta-clustering	meta.SubClustering meta.TestSubCluster
Acessors and Methods for immunoClust Objects	aposteriori,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 Objects	addLevel<- 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_names,immunoMeta-method sam_names.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 Results	plot,immunoClust,missing-method plot,immunoClust-method plot.immunoClust
Scatterplot of immunoMeta Structured Clustering Results	plot,immunoMeta,missing-method plot,immunoMeta-method plot.immunoMeta
Scatterplot Matrix of immunoClust Clustering Results	datSplom splom splom,immunoClust,flowFrame-method splom,immunoClust,matrix-method splom,immunoClust,missing-method splom.immunoClust
immunoClust asinh-Transformation	trans.ApplyToData
immunoClust asinh-Transformation Optimization	trans.FitToData