coseq: Co-Expression Analysis of Sequencing Data
Version 0.99.0

Gaussian and Poisson mixture models are implemented to cluster biological entities (e.g., genes) from high-throughput sequencing data. Parameter estimation is performed using the EM algorithm and model selection criteria (to choose the number of clusters) are provided.

AuthorAndrea Rau, Cathy Maugis-Rabusseau
Bioconductor views GeneExpression RNASeq Sequencing Software
Date of publication2016-09-24 20:15:58
MaintainerAndrea Rau <andrea.rau@jouy.inra.fr>
LicenseGPL (>=3)
Version0.99.0
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("coseq", repos="http://R-Forge.R-project.org")

Getting started

Package overview
*coseq* package instructions"

Popular man pages

coseq: Co-expression or co-abudance analysis of high-throughput...
coseq-package: Co-expression and co-abundance analysis of high-throughput...
coseq_run: Co-expression analysis
coseqUsersGuide: View coseq User's Guide
summary.NormMixClus: Summarize results from clustering using a Normal mixture...
summary.PoisMixClus: Summarize results from clustering using a Poisson mixture...
transform_RNAseq: Transform RNA-seq data using common transformations
See all...

All man pages Function index File listing

Man pages

clusterEntropy: Calculation of per-cluster entropy
compareARI: Pairwise comparisons of ARI values among a set of clustering...
compareICL: Compare corrected ICL values after data transformation
coseq: Co-expression or co-abudance analysis of high-throughput...
coseq-package: Co-expression and co-abundance analysis of high-throughput...
coseq_run: Co-expression analysis
coseqUsersGuide: View coseq User's Guide
matchContTable: Permute columns of a contingency table
NormMixClus: Normal mixture model estimation and selection for a series of...
NormMixClus_K: Normal mixture model estimation
NormMixParam: Calculate the mean and covariance for a Normal mixture model
plot.coseq: Visualize results from coseq clustering
plot.NormMixClus: Visualize results from clustering using a Normal mixture...
plot.NormMixClus_K: Plot NormMixClus_K object
plot.PoisMixClus: Visualize results from clustering using a Poisson mixture...
summary.coseq: Summarize results from clustering using a Poisson or Gaussian...
summary.NormMixClus: Summarize results from clustering using a Normal mixture...
summary.NormMixClus_K: Summarize results from clustering using a Normal mixture...
summary.PoisMixClus: Summarize results from clustering using a Poisson mixture...
transform_RNAseq: Transform RNA-seq data using common transformations

Functions

NormMixClus Man page Source code
NormMixClus_K Man page Source code
NormMixParam Man page Source code
clusterEntropy Man page Source code
compareARI Man page Source code
compareICL Man page Source code
coseq Man page Source code
coseq-package Man page
coseq.DESeqDataSet Man page Source code
coseq.data.frame Man page Source code
coseq.matrix Man page Source code
coseqUsersGuide Man page Source code
coseq_run Man page Source code
matchContTable Man page Source code
plot.NormMixClus Man page Source code
plot.NormMixClus_K Man page Source code
plot.PoisMixClus Man page Source code
plot.coseq Man page Source code
summary.NormMixClus Man page Source code
summary.NormMixClus_K Man page
summary.PoisMixClus Man page Source code
summary.coseq Man page Source code
transform_RNAseq Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/NormMixClus.R
R/NormMixClus_K.R
R/NormMixParam.R
R/clusterEntropy.R
R/compareARI.R
R/compareICL.R
R/coseq-methods.R
R/coseq-package.R
R/coseqUsersGuide.R
R/coseq_run.R
R/matchContTable.R
R/plot.NormMixClus.R
R/plot.NormMixClus_K.R
R/plot.PoisMixClus.R
R/plot.coseq.R
R/summary.NormMixClus.R
R/summary.NormMixClus_K.R
R/summary.PoisMixClus.R
R/summary.coseq.R
R/transform_RNAseq.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/coseq.Rmd
inst/doc/coseq.html
inst/doc/coseqUsersGuide.pdf
inst/examples
inst/examples/NormMixClus.R
inst/examples/PoisMixClus_ex.R
inst/examples/coseq-package.R
man
man/NormMixClus.Rd
man/NormMixClus_K.Rd
man/NormMixParam.Rd
man/clusterEntropy.Rd
man/compareARI.Rd
man/compareICL.Rd
man/coseq-package.Rd
man/coseq.Rd
man/coseqUsersGuide.Rd
man/coseq_run.Rd
man/matchContTable.Rd
man/plot.NormMixClus.Rd
man/plot.NormMixClus_K.Rd
man/plot.PoisMixClus.Rd
man/plot.coseq.Rd
man/summary.NormMixClus.Rd
man/summary.NormMixClus_K.Rd
man/summary.PoisMixClus.Rd
man/summary.coseq.Rd
man/transform_RNAseq.Rd
vignettes
vignettes/coseq.Rmd
coseq documentation built on May 21, 2017, 12:52 a.m.

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