Package: flowClust 3.45.0
Greg Finak
flowClust: Clustering for Flow Cytometry
Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'.
Authors:
flowClust_3.45.0.tar.gz
flowClust_3.45.0.zip(r-4.5)flowClust_3.45.0.zip(r-4.4)flowClust_3.45.0.zip(r-4.3)
flowClust_3.45.0.tgz(r-4.4-x86_64)flowClust_3.45.0.tgz(r-4.4-arm64)flowClust_3.45.0.tgz(r-4.3-x86_64)flowClust_3.45.0.tgz(r-4.3-arm64)
flowClust_3.45.0.tar.gz(r-4.5-noble)flowClust_3.45.0.tar.gz(r-4.4-noble)
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flowClust.pdf |flowClust.html✨
flowClust/json (API)
NEWS
| # Install 'flowClust' in R: |
| install.packages('flowClust', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- rituximab - The Rituximab Dataset
On BioConductor:flowClust-3.45.0(bioc 3.21)flowClust-3.44.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologyclusteringvisualizationflowcytometry
Last updated 2 months agofrom:ace5f62100. Checks:OK: 1 WARNING: 6 ERROR: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 29 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 29 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 29 2024 |
| R-4.4-mac-x86_64 | WARNING | Nov 29 2024 |
| R-4.4-mac-aarch64 | WARNING | Nov 29 2024 |
| R-4.3-win-x86_64 | WARNING | Nov 29 2024 |
| R-4.3-mac-x86_64 | ERROR | Oct 30 2024 |
| R-4.3-mac-aarch64 | ERROR | Oct 30 2024 |
Exports:%in%boxcriterioncriterion<-densitydmvtdmvtmixflowClustgetEstimatesimportanceMapplotposteriorrboxruleOutliersruleOutliers<-showsplitSubsetsummarizeFiltersummarytmixFilteruncertainty
Dependencies:BHBiobaseBiocGenericscpp11cytolibflowCoregenericsgraphmatrixStatsRcppRhdf5libRProtoBufLibS4Vectors
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Clustering for Flow Cytometry | flowClust-package |
| Extract the BIC for a flowClust fit. | BIC BIC.flowClust BIC.flowClustList |
| Box-Cox Transformation | box |
| Various Functions for Retrieving Information from Clustering Results | criterion criterion,flowClust-method criterion,flowClustList-method criterion<- criterion<-,flowClustList,character-method getEstimates importance posterior uncertainty |
| Density of the Multivariate t Distribution with Box-Cox Tranformation | dmvt |
| Density of the Multivariate t Mixture Distribution with Box-Cox Tranformation | dmvtmix |
| Robust Model-based Clustering for Flow Cytometry | flowClust flowClust-class flowClustList-class fowClust |
| generate the curve that reflects the tmixture fitting outcome | flowClust.den |
| Grid of Density Values for the Fitted t Mixture Model with Box-Cox Transformation | density,flowClust-method density,flowClustList-method density-method density.flowClust flowDens-class |
| 1-D Density Plot (Histogram) of Clustering Results | hist.flowClust hist.flowClustList |
| Cluster Assignment Based on Clustering Results | Map Map,flowClust-method Map,flowClustList-method Map.flowClust |
| Scatterplot of Clustering Results | plot plot,flowClust,missing-method plot,flowClust-method plot,flowClustList,missing-method |
| Contour or Image Plot of Clustering Results | plot,flowDens,missing-method plot,flowDens-method plot.flowDens |
| Scatterplot / 1-D Density Plot of Filtering (Clustering) Results | plot,flowFrame,tmixFilterResult-method plot,flowFrame,tmixFilterResultList-method plot,tmixFilterResult-method plot.flowFrame plot.flowFrame.tmixFilterResult plot.tmixFilterResult |
| Reverse Box-Cox Transformation | rbox |
| The Rituximab Dataset | rituximab |
| Showing or Modifying the Rule used to Identify Outliers | ruleOutliers ruleOutliers,flowClust-method ruleOutliers,flowClustList-method ruleOutliers.flowClust ruleOutliers<- ruleOutliers<-,flowClust,list-method ruleOutliers<-,flowClustList,list-method |
| Show Method for flowClust / tmixFilterResult Object | show,flowClust-method show,flowClustList-method show,tmixFilter-method show,tmixFilterResult-method show,tmixFilterResultList-method show.flowClust show.tmixFilterResult |
| Splitting Data Based on Clustering Results | split split,data.frame,flowClust-method split,data.frame,flowClustList-method split,flowClust-method split,flowFrame,flowClust-method split,flowFrame,flowClustList-method split,flowFrame,tmixFilterResult-method split,flowFrame,tmixFilterResultList-method split,matrix,flowClust-method split,matrix,flowClustList-method split,vector,flowClust-method split,vector,flowClustList-method split.flowClust split.flowFrame split.tmixFilterResult |
| Subsetting Data Based on Clustering Results | Subset Subset,ANY,flowClustList-method Subset,data.frame,flowClust-method Subset,flowClust-method Subset,flowFrame,flowClust-method Subset,flowFrame,tmixFilterResult-method Subset,flowFrame,tmixFilterResultList-method Subset,matrix,flowClust-method Subset,vector,flowClust-method Subset.flowClust Subset.flowFrame Subset.flowFrame.tmixFilterResult Subset.tmixFilterResult |
| Summary Method for flowClust Object | summary summary,flowClust-method summary,flowClustList-method summary,tmixFilterResult-method summary,tmixFilterResultList-method summary.flowClust summary.tmixFilterResult |
| Creating Filters and Filtering Flow Cytometry Data | %in%,ANY,flowClust-method %in%,ANY,flowClustList-method %in%,ANY,tmixFilterResult-method %in%,ANY,tmixFilterResultList-method %in%,flowFrame,tmixFilter-method %in%,flowFrame,tmixFilterResult-method length,tmixFilterResultList-method summarizeFilter,tmixFilterResult,tmixFilter-method tmixFilter tmixFilter-class tmixFilterResult-class tmixFilterResultList tmixFilterResultList-class [,flowFrame,flowClust-method [,flowFrame,flowClustList-method [,flowFrame,tmixFilterResult-method [,flowFrame,tmixFilterResultList-method [[,tmixFilterResultList,ANY-method |
