Package: immunoClust 1.39.3
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:
immunoClust_1.39.3.tar.gz
immunoClust_1.39.3.zip(r-4.5)immunoClust_1.39.3.zip(r-4.4)immunoClust_1.39.3.zip(r-4.3)
immunoClust_1.39.3.tgz(r-4.4-x86_64)immunoClust_1.39.3.tgz(r-4.4-arm64)immunoClust_1.39.3.tgz(r-4.3-x86_64)immunoClust_1.39.3.tgz(r-4.3-arm64)
immunoClust_1.39.3.tar.gz(r-4.5-noble)immunoClust_1.39.3.tar.gz(r-4.4-noble)
immunoClust_1.39.0.tgz(r-4.4-emscripten)immunoClust_1.39.3.tgz(r-4.3-emscripten)
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')) |
On BioConductor:immunoClust-1.39.3(bioc 3.21)immunoClust-1.38.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
clusteringflowcytometrysinglecellcellbasedassaysimmunooncologygslcpp
Last updated 1 months agofrom:17b4bb8e09. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 26 2024 |
| R-4.5-win-x86_64 | OK | Dec 26 2024 |
| R-4.5-linux-x86_64 | OK | Dec 26 2024 |
| R-4.4-win-x86_64 | OK | Dec 26 2024 |
| R-4.4-mac-x86_64 | OK | Dec 26 2024 |
| R-4.4-mac-aarch64 | OK | Dec 26 2024 |
| R-4.3-win-x86_64 | OK | Dec 26 2024 |
| R-4.3-mac-x86_64 | OK | Nov 26 2024 |
| R-4.3-mac-aarch64 | OK | Nov 26 2024 |
Exports:addLevel<-aposterioribhattacharyya.coeffbhattacharyya.distbhattacharyya.probcell.Classifycell.classifyAllcell.ClustDatacell.EMstepcell.EMtcell.Estepcell.FitModelcell.hclustcell.InitialModelcell.MajorIterationLoopcell.MajorIterationTranscell.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:BHBiobaseBiocGenericscpp11cytolibflowCoregenericslatticematrixStatsRcppRhdf5libRProtoBufLibS4Vectors
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_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_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 |