flowClust: Clustering for Flow Cytometry

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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'.

Author
Raphael Gottardo <raph@stat.ubc.ca>, Kenneth Lo <c.lo@stat.ubc.ca>, Greg Finak <gfinak@fhcrc.org>
Date of publication
None
Maintainer
Greg Finak <gfinak@fhcrc.org>, Mike Jiang <wjiang2@fhcrc.org>
License
Artistic-2.0
Version
3.12.1

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

Files in this package

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