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

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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).

Author
Andrea Rau, Gilles Celeux, Marie-Laure Martin-Magniette, Cathy Maugis- Rabusseau
Date of publication
2016-05-26 22:05:04
Maintainer
Andrea Rau <andrea.rau@jouy.inra.fr>
License
GPL (>= 3)
Version
2.0.8

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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...

Files in this package

HTSCluster
HTSCluster/inst
HTSCluster/inst/CITATION
HTSCluster/inst/NEWS
HTSCluster/inst/doc
HTSCluster/inst/doc/HTSCluster.pdf
HTSCluster/inst/doc/HTSCluster.Rnw
HTSCluster/inst/doc/HTSCluster.R
HTSCluster/inst/doc/HTSClusterUsersGuide.pdf
HTSCluster/NAMESPACE
HTSCluster/R
HTSCluster/R/logLikePoisMixDiff.R
HTSCluster/R/plot.HTSClusterWrapper.R
HTSCluster/R/emInit.R
HTSCluster/R/kmeanInit.R
HTSCluster/R/HTSClusterUsersGuide.R
HTSCluster/R/PoisMixClus.R
HTSCluster/R/plot.HTSCluster.R
HTSCluster/R/summary.HTSCluster.R
HTSCluster/R/probaPostInit.R
HTSCluster/R/PoisMixMean.R
HTSCluster/R/probaPost.R
HTSCluster/R/HTSCluster-internal.R
HTSCluster/R/mylogLikePoisMixObs.R
HTSCluster/R/logLikePoisMix.R
HTSCluster/R/PoisMixSim.R
HTSCluster/R/highDimensionARI.R
HTSCluster/R/splitEMInit.R
HTSCluster/R/PoisMixClusWrapper.R
HTSCluster/R/summary.HTSClusterWrapper.R
HTSCluster/vignettes
HTSCluster/vignettes/HTSCluster.Rnw
HTSCluster/MD5
HTSCluster/build
HTSCluster/build/vignette.rds
HTSCluster/DESCRIPTION
HTSCluster/man
HTSCluster/man/PoisMixSim.Rd
HTSCluster/man/PoisMixMean.Rd
HTSCluster/man/HTSCluster-package.Rd
HTSCluster/man/logLikePoisMix.Rd
HTSCluster/man/summary.HTSCluster.Rd
HTSCluster/man/HTSClusterUsersGuide.Rd
HTSCluster/man/plot.HTSCluster.Rd
HTSCluster/man/Init.Rd
HTSCluster/man/PoisMixClus.Rd
HTSCluster/man/probaPost.Rd
HTSCluster/man/highDimensionARI.Rd