Package: flowClust 3.51.0

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:Raphael Gottardo, Kenneth Lo <[email protected]>, Greg Finak <[email protected]>

flowClust_3.51.0.tar.gz
flowClust_3.51.0.zip(r-4.7)flowClust_3.51.0.zip(r-4.6)flowClust_3.51.0.zip(r-4.5)
flowClust_3.51.0.tgz(r-4.6-x86_64)flowClust_3.51.0.tgz(r-4.6-arm64)flowClust_3.51.0.tgz(r-4.5-x86_64)flowClust_3.51.0.tgz(r-4.5-arm64)
flowClust_3.51.0.tar.gz(r-4.7-arm64)flowClust_3.51.0.tar.gz(r-4.7-x86_64)flowClust_3.51.0.tar.gz(r-4.6-arm64)flowClust_3.51.0.tar.gz(r-4.6-x86_64)
flowClust_3.51.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
flowClust/json (API)

# Install 'flowClust' in R:

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

Datasets:

rituximab - The Rituximab Dataset

On BioConductor:flowClust-3.51.0(bioc 3.24)flowClust-3.50.0(bioc 3.23)

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

immunooncology clustering visualization flowcytometry

7.26 score 7 packages 87 scripts 33 mentions 23 exports 16 dependencies

Last updated from:66e3c7f05d. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	402
linux-devel-arm64	WARNING	444
linux-devel-x86_64	WARNING	733
source / vignettes	OK	533
linux-release-arm64	WARNING	449
linux-release-x86_64	WARNING	515
macos-release-arm64	WARNING	284
macos-release-x86_64	WARNING	688
macos-oldrel-arm64	WARNING	350
macos-oldrel-x86_64	WARNING	531
windows-devel	WARNING	336
windows-release	WARNING	338
windows-oldrel	WARNING	406
wasm-release	OK	931

Exports:%in%box criterion criterion<-density dmvt dmvtmix flowClust getEstimates importance Map plot posterior rbox ruleOutliers ruleOutliers<-show split Subset summarizeFilter summary tmixFilter uncertainty

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

Robust Model-based Clustering of Flow Cytometry Data The flowClust package

Rendered fromflowClust.Rmdusingknitr::rmarkdown

Last update: 2022-03-15
Started: 2019-04-04

Citation

Development and contributors

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