immunoClust: immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
Version 1.8.0

Model based clustering and meta-clustering of Flow Cytometry Data

Browse man pages Browse package API and functions Browse package files

AuthorTill Soerensen <till-antoni.soerensen@charite.de>
Bioconductor views CellBasedAssays Clustering FlowCytometry
Date of publicationNone
MaintainerTill Soerensen <till-antoni.soerensen@charite.de>
LicenseArtistic-2.0
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("immunoClust")

Man pages

cell.ClustData: Model Based Clustering of Data for a pre-defined Number of...
cell.EM: immunoClust EMt-iteration on Cell-events given initial Model...
cell.FitModel: immunoClust EMt-iteration on Cell-events given initial Model...
cell.hclust: Hierarchical Model Based Clustering of Cell-events in the...
cell.ME: immunoClust EM-iteration on Cell-events given initial Cluster...
cell.process: Clustering of Cell-events in the immunoClust-pipeline
cell.removed: Brief Information of removed Cell-events by immunoClust...
cell.SubClustering: immunoClust Model Refinement Step in iterative Cell-events...
dat.exp: immunoClust Meta-clustering Sample
dat.fcs: immunoClust Cell-clustering Sample
dat.meta: immunoClust Meta-clustering Results Sample
immunoClust.object: immunoClust-Object
immunoClust-package: immunoClust - Automated Pipeline for Population Detection in...
meta.clustering: Clustering of Cell-clusters in the immunoClust-pipeline
meta.export: immunoClust Meta-clustering Results Export
meta.exprs: Collecting Data of an immunoClust vector
meta.hclust: Hierarchical Meta-clustering of Cell-clusters in the...
meta.ME: immunoClust EM(t)-iteration on Cell-clusters
meta.normalize: immunoClust normalization step with the meta.clustering...
meta.plot: Ploting of immunoClust Meta-clustering Results
meta.process: Meta-clustering of Cell-clusters in the immunoClust-pipeline
meta.regnorm: immunoClust normalization procedure
meta.SubClustering: immunoClust Model Refinement Step in iterative...
plot.immunoClust: Scatterplot of immunoClust Clustering Results
splom.immunoClust: Scatterplot Matrix of immunoClust Clustering Results
trans.ApplyToData: immunoClust asinh-Transformation
trans.FitToData: immunoClust asinh-Transformation Optimization

Functions

cell.Classify Man page Source code
cell.ClustData Man page Source code
cell.EM Man page Source code
cell.Estimation Man page Source code
cell.FitModel Man page Source code
cell.InitialModel Man page Source code
cell.ME Man page Source code
cell.MajorIterationLoop Man page Source code
cell.MajorIterationTrans Man page Source code
cell.SubClustering Man page Source code
cell.TestSubCluster Man page Source code
cell.classifyAll Man page Source code
cell.compensate Source code
cell.hclust Man page Source code
cell.process Man page Source code
cl_delta Source code
cl_delta2 Source code
cl_lambda Source code
classification.matrices Source code
classification.max Source code
classification.maximization Source code
classification.score Source code
classification.separation Source code
cls_colors Source code
clust.hclass Source code
clust.hpairs2 Source code
clust.mergedClusters Source code
clust.panel.splom Source code
clust.panel.xyplot Source code
clust.partconv Source code
clust.prepanel Source code
clusterData Source code
clusterInclude Source code
dat.exp Man page
dat.fcs Man page
dat.meta Man page
datSplom Man page Source code
ellipse.panel.splom Source code
ellipse.panel.xyplot Source code
ellipsePoints Source code
exprs Source code
immunoClust Man page
immunoClust-class Man page
immunoClust-package Man page
immunoClust.object Man page
immunoClust.package Man page
mergeModel Source code
meta.Clustering Man page Source code
meta.ClustersForScatter Source code
meta.ME Man page Source code
meta.Normalize Man page Source code
meta.RegNorm Man page Source code
meta.SubClustering Man page Source code
meta.TestSubCluster Man page Source code
meta.clsGate Source code
meta.export Man page
meta.exprs Man page Source code
meta.freqGate Source code
meta.freqTable Man page Source code
meta.gating Source code
meta.getGate Source code
meta.hclust Man page Source code
meta.majorEvents Man page Source code
meta.numClusters Man page Source code
meta.numEvents Man page Source code
meta.numGate Source code
meta.parGate Source code
meta.parMFI Man page Source code
meta.plotClusters Man page Source code
meta.plotClustersForScatter Man page Source code
meta.plotExpClusters Man page Source code
meta.plotExpResult Man page Source code
meta.plotGate Man page Source code
meta.plotGating Man page Source code
meta.plotScatter Man page Source code
meta.posterior.gating Source code
meta.process Man page Source code
meta.relEvents Man page Source code
meta.relEvents2 Man page Source code
meta.relEvents3 Man page Source code
meta.scatter.gating Source code
meta.scatter.prior.6 Source code
meta.scatter.prior.7 Source code
meta.setGate Source code
minDelta Source code
mmunoClust2 Source code
plot Man page
plot,immunoClust,missing-method Man page
plot,immunoClust-method Man page
plot.immunoClust Man page Man page
removed.above Man page Source code
removed.below Man page Source code
separateX Source code
separation.max Source code
separation.maximization Source code
separation.score Source code
show Man page
show,immunoClust-method Man page
show.immunoClust Man page
splom Man page
splom,immunoClust,flowFrame-method Man page
splom,immunoClust,matrix-method Man page
splom,immunoClust,missing-method Man page
splom.immunoClust Man page
summary Man page
summary,immunoClust-method Man page
summary.immunoClust Man page
trans.ApplyToData Man page Source code
trans.FitToData Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/cell.clustering.R
R/class.immunoClust.R
R/clust.util.R
R/data.R
R/meta.clustering.R
R/meta.export.R
R/meta.gating.R
R/meta.plot.R
R/plot.immunoClust.R
R/process.R
R/splom.immunoClust.R
R/transform.R
a.out.dSYM
a.out.dSYM/Contents
a.out.dSYM/Contents/Info.plist
a.out.dSYM/Contents/Resources
a.out.dSYM/Contents/Resources/DWARF
a.out.dSYM/Contents/Resources/DWARF/a.out
aclocal.m4
build
build/vignette.rds
cleanup
configure
configure.ac
data
data/dat.exp.RData
data/dat.fcs.RData
data/dat.meta.RData
inst
inst/doc
inst/doc/immunoClust.R
inst/doc/immunoClust.Rnw
inst/doc/immunoClust.pdf
man
man/cell.ClustData.Rd
man/cell.EM.Rd
man/cell.FitModel.Rd
man/cell.ME.Rd
man/cell.SubClustering.Rd
man/cell.hclust.Rd
man/cell.process.Rd
man/cell.removed.Rd
man/dat.exp.Rd
man/dat.fcs.Rd
man/dat.meta.Rd
man/immunoClust-package.Rd
man/immunoClust.object.Rd
man/meta.ME.Rd
man/meta.SubClustering.Rd
man/meta.clustering.Rd
man/meta.export.Rd
man/meta.exprs.Rd
man/meta.hclust.Rd
man/meta.normalize.Rd
man/meta.plot.Rd
man/meta.process.Rd
man/meta.regnorm.Rd
man/plot.immunoClust.Rd
man/splom.immunoClust.Rd
man/trans.ApplyToData.Rd
man/trans.FitToData.Rd
src
src/Makevars.in
src/Makevars.win
src/R_meta.cpp
src/R_model.cpp
src/dist_mvn.cpp
src/dist_mvn.h
src/em_meta.cpp
src/em_meta.h
src/em_mvn.cpp
src/em_mvn.h
src/em_mvt.cpp
src/em_mvt.h
src/hc_meta.cpp
src/hc_meta.h
src/hc_mvn.cpp
src/hc_mvn.h
src/immunoClust.c
src/immunoClust.h
src/meta_gpa.cpp
src/meta_gpa.h
src/meta_norm.cpp
src/meta_norm.h
src/meta_scale.cpp
src/meta_scale.h
src/normalize.cpp
src/normalize.h
src/sub_mvn.cpp
src/sub_mvn.h
src/util.cpp
src/util.h
src/vs_htrans.cpp
src/vs_htrans.h
vignettes
vignettes/immunoClust.Rnw
immunoClust documentation built on May 20, 2017, 10:42 p.m.