coseq: Co-Expression Analysis of Sequencing Data

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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.

Author
Andrea Rau, Cathy Maugis-Rabusseau
Date of publication
2016-09-24 20:15:58
Maintainer
Andrea Rau <andrea.rau@jouy.inra.fr>
License
GPL (>=3)
Version
0.99.0

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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

Files in this package

coseq/DESCRIPTION
coseq/NAMESPACE
coseq/R
coseq/R/NormMixClus.R
coseq/R/NormMixClus_K.R
coseq/R/NormMixParam.R
coseq/R/clusterEntropy.R
coseq/R/compareARI.R
coseq/R/compareICL.R
coseq/R/coseq-methods.R
coseq/R/coseq-package.R
coseq/R/coseqUsersGuide.R
coseq/R/coseq_run.R
coseq/R/matchContTable.R
coseq/R/plot.NormMixClus.R
coseq/R/plot.NormMixClus_K.R
coseq/R/plot.PoisMixClus.R
coseq/R/plot.coseq.R
coseq/R/summary.NormMixClus.R
coseq/R/summary.NormMixClus_K.R
coseq/R/summary.PoisMixClus.R
coseq/R/summary.coseq.R
coseq/R/transform_RNAseq.R
coseq/build
coseq/build/vignette.rds
coseq/inst
coseq/inst/CITATION
coseq/inst/NEWS
coseq/inst/doc
coseq/inst/doc/coseq.Rmd
coseq/inst/doc/coseq.html
coseq/inst/doc/coseqUsersGuide.pdf
coseq/inst/examples
coseq/inst/examples/NormMixClus.R
coseq/inst/examples/PoisMixClus_ex.R
coseq/inst/examples/coseq-package.R
coseq/man
coseq/man/NormMixClus.Rd
coseq/man/NormMixClus_K.Rd
coseq/man/NormMixParam.Rd
coseq/man/clusterEntropy.Rd
coseq/man/compareARI.Rd
coseq/man/compareICL.Rd
coseq/man/coseq-package.Rd
coseq/man/coseq.Rd
coseq/man/coseqUsersGuide.Rd
coseq/man/coseq_run.Rd
coseq/man/matchContTable.Rd
coseq/man/plot.NormMixClus.Rd
coseq/man/plot.NormMixClus_K.Rd
coseq/man/plot.PoisMixClus.Rd
coseq/man/plot.coseq.Rd
coseq/man/summary.NormMixClus.Rd
coseq/man/summary.NormMixClus_K.Rd
coseq/man/summary.PoisMixClus.Rd
coseq/man/summary.coseq.Rd
coseq/man/transform_RNAseq.Rd
coseq/vignettes
coseq/vignettes/coseq.Rmd