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'.

AuthorRaphael Gottardo <raph@stat.ubc.ca>, Kenneth Lo <c.lo@stat.ubc.ca>, Greg Finak <gfinak@fhcrc.org>
Date of publicationNone
MaintainerGreg Finak <gfinak@fhcrc.org>, Mike Jiang <wjiang2@fhcrc.org>
LicenseArtistic-2.0
Version3.12.2

View on Bioconductor

Man pages

box: Box-Cox Transformation

density: Grid of Density Values for the Fitted t Mixture Model with...

dmvt: Density of the Multivariate t Distribution with Box-Cox...

dmvtmix: Density of the Multivariate t Mixture Distribution with...

flowClust: Robust Model-based Clustering for Flow Cytometry

flowClust2Prior: Generate a prior specification based on a flowClust model...

flowClust.den: generate the curve that reflects the tmixture fitting outcome

flowClust-package: Clustering for Flow Cytometry

hist: 1-D Density Plot (Histogram) of Clustering Results

Map: Cluster Assignment Based on Clustering Results

miscellaneous: Various Functions for Retrieving Information from Clustering...

mkPrior: Generate a flowClust prior specification

peakMatch: Function to match peaks across samples

plot.flowClust: Scatterplot of Clustering Results

plot.flowCore: Scatterplot / 1-D Density Plot of Filtering (Clustering)...

plot.flowDens: Contour or Image Plot of Clustering Results

plotPrior: Plots a flowClust prior over some data.

rbox: Reverse Box-Cox Transformation

rituximab: The Rituximab Dataset

ruleOutliers: Showing or Modifying the Rule used to Identify Outliers

show.flowClust: Show Method for flowClust / tmixFilterResult Object

SimulateMixture: Random Generation from a t Mixture Model with Box-Cox...

split: Splitting Data Based on Clustering Results

Subset: Subsetting Data Based on Clustering Results

summary: Summary Method for flowClust Object

tmixFilter: Creating Filters and Filtering Flow Cytometry Data

Functions

box Man page
criterion Man page
criterion<- Man page
criterion<-,flowClustList,character-method Man page
criterion,flowClustList-method Man page
criterion,flowClust-method Man page
density.flowClust Man page
density,flowClustList-method Man page
density,flowClust-method Man page
density-method Man page
dmvt Man page
dmvtmix Man page
flowClust Man page
flowClust2Prior Man page
flowClust-class Man page
flowClust.den Man page
flowClustList-class Man page
flowClust-package Man page
flowDens-class Man page
[,flowFrame,flowClust,ANY,ANY-method Man page
[,flowFrame,flowClustList,ANY,ANY-method Man page
[,flowFrame,tmixFilterResult,ANY,ANY-method Man page
[,flowFrame,tmixFilterResultList,ANY,ANY-method Man page
fowClust Man page
getEstimates Man page
hist.flowClust Man page
hist.flowClustList Man page
importance Man page
\%in\%,ANY,flowClustList-method Man page
\%in\%,ANY,flowClust-method Man page
\%in\%,ANY,tmixFilterResultList-method Man page
\%in\%,ANY,tmixFilterResult-method Man page
\%in\%,flowFrame,tmixFilter-method Man page
\%in\%,flowFrame,tmixFilterResult-method Man page
length,tmixFilterResultList-method Man page
Map Man page
Map.flowClust Man page
Map,flowClustList-method Man page
Map,flowClust-method Man page
mkPrior Man page
mkPrior,list,flowSet,ANY,missing-method Man page
mkPrior,list,flowSet,missing,missing-method Man page
mkPrior,missing,flowFrame,missing,missing-method Man page
mkPrior,missing,flowSet,ANY,missing-method Man page
mkPrior,polygonGate,flowFrame,missing,missing-method Man page
mkPrior,polygonGate,flowFrame,numeric,matrix-method Man page
mkPrior,rectangleGate,flowFrame,missing,missing-method Man page
mkPrior,rectangleGate,flowFrame,numeric,matrix-method Man page
peakMatch Man page
plot Man page
plot,flowClustList,missing-method Man page
plot,flowClust-method Man page
plot,flowClust,missing-method Man page
plot.flowDens Man page
plot,flowDens-method Man page
plot,flowDens,missing-method Man page
plot.flowFrame Man page
plot.flowFrame.tmixFilterResult Man page
plot,flowFrame,tmixFilterResultList-method Man page
plot,flowFrame,tmixFilterResult-method Man page
plotPrior Man page
plot.tmixFilterResult Man page
plot,tmixFilterResult-method Man page
posterior Man page
rbox Man page
rituximab Man page
ruleOutliers Man page
ruleOutliers<- Man page
ruleOutliers.flowClust Man page
ruleOutliers<-,flowClustList,list-method Man page
ruleOutliers<-,flowClust,list-method Man page
ruleOutliers,flowClustList-method Man page
ruleOutliers,flowClust-method Man page
show.flowClust Man page
show,flowClustList-method Man page
show,flowClust-method Man page
show,tmixFilter-method Man page
show.tmixFilterResult Man page
show,tmixFilterResultList-method Man page
show,tmixFilterResult-method Man page
SimulateMixture Man page
split Man page
split,data.frame,flowClustList-method Man page
split,data.frame,flowClust-method Man page
split.flowClust Man page
split,flowClust-method Man page
split.flowFrame Man page
split,flowFrame,flowClustList-method Man page
split,flowFrame,flowClust-method Man page
split,flowFrame,tmixFilterResultList-method Man page
split,flowFrame,tmixFilterResult-method Man page
split,matrix,flowClustList-method Man page
split,matrix,flowClust-method Man page
split.tmixFilterResult Man page
split,vector,flowClustList-method Man page
split,vector,flowClust-method Man page
Subset Man page
Subset,ANY,flowClustList-method Man page
Subset,data.frame,flowClust-method Man page
Subset.flowClust Man page
Subset,flowClust-method Man page
Subset.flowFrame Man page
Subset,flowFrame,flowClust-method Man page
Subset.flowFrame.tmixFilterResult Man page
Subset,flowFrame,tmixFilterResultList-method Man page
Subset,flowFrame,tmixFilterResult-method Man page
Subset,matrix,flowClust-method Man page
Subset.tmixFilterResult Man page
Subset,vector,flowClust-method Man page
summarizeFilter,tmixFilterResult,tmixFilter-method Man page
summary Man page
summary.flowClust Man page
summary,flowClustList-method Man page
summary,flowClust-method Man page
summary.tmixFilterResult Man page
summary,tmixFilterResultList-method Man page
summary,tmixFilterResult-method Man page
tmixFilter Man page
tmixFilter-class Man page
tmixFilterResult-class Man page
tmixFilterResultList Man page
[[,tmixFilterResultList,ANY-method Man page
tmixFilterResultList-class Man page
uncertainty Man page

Files

flowClust/DESCRIPTION
flowClust/NAMESPACE
flowClust/NEWS
flowClust/R
flowClust/R/SetClasses.R flowClust/R/SetMethods.R flowClust/R/SimulateMixture.R flowClust/R/coerce.R flowClust/R/flowClust-package.R flowClust/R/flowClust.R flowClust/R/hist.R flowClust/R/miscellaneous.R flowClust/R/mkPriors.R flowClust/R/peakMatch.R flowClust/R/plot.R flowClust/R/split.R
flowClust/README
flowClust/README.md
flowClust/aclocal.m4
flowClust/build
flowClust/build/vignette.rds
flowClust/cleanup
flowClust/configure
flowClust/configure.ac
flowClust/data
flowClust/data/rituximab.RData
flowClust/inst
flowClust/inst/CITATION
flowClust/inst/README
flowClust/inst/doc
flowClust/inst/doc/flowClust.R
flowClust/inst/doc/flowClust.Rnw
flowClust/inst/doc/flowClust.pdf
flowClust/man
flowClust/man/Map.Rd flowClust/man/SimulateMixture.Rd flowClust/man/Subset.Rd flowClust/man/box.Rd flowClust/man/density.Rd flowClust/man/dmvt.Rd flowClust/man/dmvtmix.Rd flowClust/man/flowClust-package.Rd flowClust/man/flowClust.Rd flowClust/man/flowClust.den.Rd flowClust/man/flowClust2Prior.Rd flowClust/man/hist.Rd flowClust/man/miscellaneous.Rd flowClust/man/mkPrior.Rd flowClust/man/peakMatch.Rd flowClust/man/plot.flowClust.Rd flowClust/man/plot.flowCore.Rd flowClust/man/plot.flowDens.Rd flowClust/man/plotPrior.Rd flowClust/man/rbox.Rd flowClust/man/rituximab.Rd flowClust/man/ruleOutliers.Rd flowClust/man/show.flowClust.Rd flowClust/man/split.Rd flowClust/man/summary.Rd flowClust/man/tmixFilter.Rd
flowClust/src
flowClust/src/BoxCox.c
flowClust/src/BoxCoxPriors.c
flowClust/src/Makevars.in
flowClust/src/Makevars.win
flowClust/src/Nu.c
flowClust/src/flowClust.c
flowClust/src/flowClust.h
flowClust/src/flowClustGaussian.c
flowClust/src/ranMVNT.c
flowClust/src/trim-gsl-1.13.tar.gz
flowClust/tests
flowClust/tests/testthat
flowClust/tests/testthat.R
flowClust/tests/testthat/helper-lib.R
flowClust/tests/testthat/test_1d.R
flowClust/tests/testthat/test_1d_gated_data.R
flowClust/vignettes
flowClust/vignettes/flowClust.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.