Package: flowMerge 2.55.0

Greg Finak

flowMerge: Cluster Merging for Flow Cytometry Data

Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Note: users should have a working copy of flowClust 2.0 installed.

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

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flowMerge.pdf |flowMerge.html✨
flowMerge/json (API)

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

Peer review:

Datasets:
  • flowClust.res - A flowClust model fitted to the rituximab data for 1:10 clusters.

On BioConductor:flowMerge-2.53.0(bioc 3.20)flowMerge-2.52.0(bioc 3.19)

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

immunooncologyclusteringflowcytometry

4.56 score 1 packages 6 scripts 298 downloads 6 mentions 16 exports 37 dependencies

Last updated 23 days agofrom:e5ea0ae4bd. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winWARNINGOct 30 2024
R-4.5-linuxWARNINGOct 30 2024
R-4.4-winWARNINGOct 30 2024
R-4.4-macWARNINGOct 30 2024
R-4.3-winWARNINGOct 30 2024
R-4.3-macWARNINGOct 30 2024

Exports:BICcheckForRemoteErrorsENTfitPiecewiseLinregflowObjgetDataICLmapmergeNENTpFlowMergeplotptreeshowsplitsummary

Dependencies:BHBiobaseBiocGenericscodetoolscpp11cytolibDEoptimRfeatureflowClustflowCoreFNNforeachgraphiteratorskernlabKernSmoothkslatticeMatrixmatrixStatsmclustmgcvmisc3dmulticoolmvtnormnlmepcaPPplot3DpracmaRcppRgraphvizRhdf5librobustbaseRProtoBufLibrrcovS4Vectorssnow

Merging Mixture Components for Cell Population Identification in Flow Cytometry Data The flowMerge package

Greg Finak, Raphael Gottardo

Rendered fromflowmerge.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2019-04-04
Started: 2019-04-04

Readme and manuals

Help Manual

Help pageTopics
Merging of mixture components for automated gating of flow cytometry data.flowMerge-package flowMerge
Check output of snow clusters for errorscheckForRemoteErrors
Fit Piecewise Linear Regression for a list of flowMerge ObjectsfitPiecewiseLinreg
Methods for fitPiecewiseLinreg in flowMerge packagefitPiecewiseLinreg,list-method fitPiecewiseLinreg-methods
Update the flagOutliers slot in a flowMerge objectflagOutliers
Methods to update the flagOutliers slot in a flowMerge object.flagOutliers,flowMerge-method flagOutliers-methods
A flowClust model fitted to the rituximab data for 1:10 clusters.flowClust.res RituximabFlowClustFit
Class "flowMerge"flowMerge-class getData,flowMerge-method plot,flowMerge,missing-method
Create a flowObj object from a flowClust and flowFrame objectflowObj
Class "flowObj"flowObj-class getData,flowObj-method merge,flowObj,missing-method plot,flowObj,missing-method
Initialize a SNOW cluster for use with flowMergeinitPFlowMerge
Map matrix of probabilities to class assignments.map
Merge clusters in flow cytometry datamerge merge,flowObj merge,flowObj,metric
Merge mixture componentsmerge,flowObj-methods merge-methods
Cluster merging not meant to be called by the usermergeClusters
Cluster merging not meant to be called by the usermergeClusters2
Extract the Normalized EntropyNENT
Parallelized FlowClustpFlowClust
Parellel call to flowMergepFlowMerge
Methods for plotting flowMerge and flowObj classesplot,flowMerge plot,flowObj plot-methods
Generate a Function to Plot The Merging Treeptree
Describe a flowObj or flowMerge objectshow,flowMerge-method show,flowObj-method
Split data in a flowMerge object by clustersplit,flowMerge,missing-method split-methods
Summary methods for flowMergesummary,flowMerge-method summary,flowObj-method
Update uncertaintiesupdateU