HTSCluster: Clustering High-Throughput Transcriptome Sequencing (HTS) Data
Version 2.0.8

A Poisson mixture model is implemented to cluster genes from high- throughput transcriptome sequencing (RNA-seq) data. Parameter estimation is performed using either the EM or CEM algorithm, and the slope heuristics are used for model selection (i.e., to choose the number of clusters).

AuthorAndrea Rau, Gilles Celeux, Marie-Laure Martin-Magniette, Cathy Maugis- Rabusseau
Date of publication2016-05-26 15:45:35
MaintainerAndrea Rau <andrea.rau@jouy.inra.fr>
LicenseGPL (>=3)
Version2.0.8
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("HTSCluster", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

HTSClusterUsersGuide: View HTSCluster User's Guide
Init: Parameter initialization for a Poisson mixture model.
logLikePoisMix: Log likelihood calculation for a Poisson mixture model
plot.HTSCluster: Visualize results from clustering using a Poisson mixture...
PoisMixSim: Simulate data from a Poisson mixture model
probaPost: Calculate the conditional probability of belonging to each...
summary.HTSCluster: Summarize results from clustering using a Poisson mixture...
See all...

All man pages Function index File listing

Man pages

highDimensionARI: Calculate ARI for high-dimensional data via data splits
HTSCluster-package: Clustering high throughput sequencing (HTS) data
HTSClusterUsersGuide: View HTSCluster User's Guide
Init: Parameter initialization for a Poisson mixture model.
logLikePoisMix: Log likelihood calculation for a Poisson mixture model
plot.HTSCluster: Visualize results from clustering using a Poisson mixture...
PoisMixClus: Poisson mixture model estimation and model selection
PoisMixMean: Calculate the conditional per-cluster mean of each...
PoisMixSim: Simulate data from a Poisson mixture model
probaPost: Calculate the conditional probability of belonging to each...
summary.HTSCluster: Summarize results from clustering using a Poisson mixture...

Functions

HTSCluster Man page
HTSCluster-package Man page
HTSClusterUsersGuide Man page Source code
PoisMixClus Man page Source code
PoisMixClusWrapper Man page Source code
PoisMixMean Man page Source code
PoisMixSim Man page Source code
emInit Man page Source code
highDimensionARI Man page Source code
kmeanInit Man page Source code
logLikePoisMix Man page Source code
logLikePoisMixDiff Man page Source code
myfxn Source code
mylogLikePoisMixObs Man page Source code
myloopfxn Source code
myprobafxn Source code
plot.HTSCluster Man page
plot.HTSClusterWrapper Man page Source code
probaPost Man page Source code
probaPostInit Man page Source code
splitEMInit Man page Source code
summary.HTSCluster Man page
summary.HTSClusterWrapper Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/HTSCluster-internal.R
R/HTSClusterUsersGuide.R
R/PoisMixClus.R
R/PoisMixClusWrapper.R
R/PoisMixMean.R
R/PoisMixSim.R
R/emInit.R
R/highDimensionARI.R
R/kmeanInit.R
R/logLikePoisMix.R
R/logLikePoisMixDiff.R
R/mylogLikePoisMixObs.R
R/plot.HTSCluster.R
R/plot.HTSClusterWrapper.R
R/probaPost.R
R/probaPostInit.R
R/splitEMInit.R
R/summary.HTSCluster.R
R/summary.HTSClusterWrapper.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/HTSCluster.R
inst/doc/HTSCluster.Rnw
inst/doc/HTSCluster.pdf
inst/doc/HTSClusterUsersGuide.pdf
man
man/HTSCluster-package.Rd
man/HTSClusterUsersGuide.Rd
man/Init.Rd
man/PoisMixClus.Rd
man/PoisMixMean.Rd
man/PoisMixSim.Rd
man/highDimensionARI.Rd
man/logLikePoisMix.Rd
man/plot.HTSCluster.Rd
man/probaPost.Rd
man/summary.HTSCluster.Rd
vignettes
vignettes/HTSCluster.Rnw
HTSCluster documentation built on May 21, 2017, 12:58 a.m.

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