# Co-Expression Analysis of Sequencing Data

## Documentation for package ‘coseq’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

coseq-package | Co-expression and co-abundance analysis of high-throughput sequencing data
clusterEntropy | Calculation of per-cluster entropy
clusterInertia | Calculation of within-cluster inertia
clusters | Accessors for the assigned cluster labels of a coseqResults object.
clusters-method | Accessors for the assigned cluster labels of a coseqResults object.
compareARI | Pairwise comparisons of ARI values among a set of clustering partitions
compareARI-method | Pairwise comparisons of ARI values among a set of clustering partitions
compareARI-methods | Pairwise comparisons of ARI values among a set of clustering partitions
compareICL | Compare corrected ICL values after data transformation
convertLegacyCoseq | Convert legacy coseq objects
coseq | Co-expression or co-abudance analysis of high-throughput sequencing data
coseq-method | Co-expression or co-abudance analysis of high-throughput sequencing data
coseq-methods | Co-expression or co-abudance analysis of high-throughput sequencing data
coseqFullResults | Accessors for the assigned cluster labels of a coseqResults object.
coseqFullResults-method | Accessors for the assigned cluster labels of a coseqResults object.
coseqGlobalPlots | Visualize results from coseq clustering
coseqModelPlots | Visualize results from coseq clustering
coseqResults | coseqResults object and constructor
coseqResults-class | coseqResults object and constructor
coseqRun | Co-expression analysis
DDSEextract | Accessors for the assigned cluster labels of a coseqResults object.
DDSEextract-method | Accessors for the assigned cluster labels of a coseqResults object.
Djumpextract | Accessors for the assigned cluster labels of a coseqResults object.
Djumpextract-method | Accessors for the assigned cluster labels of a coseqResults object.
fietz | RNA-seq data from the mouse neocortex in Fietz et al. (2012)
ICL | Accessors for the assigned cluster labels of a coseqResults object.
ICL-method | Accessors for the assigned cluster labels of a coseqResults object.
kmeansProbaPost | Calculate conditional probabilities of cluster membership for K-means clustering
likelihood | Accessors for the assigned cluster labels of a coseqResults object.
likelihood-method | Accessors for the assigned cluster labels of a coseqResults object.
logclr | Calculate the Log Centered Log Ratio (logCLR) transformation
matchContTable | Permute columns of a contingency table
model | Accessors for the assigned cluster labels of a coseqResults object.
model-method | Accessors for the assigned cluster labels of a coseqResults object.
nbCluster | Accessors for the assigned cluster labels of a coseqResults object.
nbCluster-method | Accessors for the assigned cluster labels of a coseqResults object.
NormMixClus | Normal mixture model estimation and selection for a series of cluster numbers
NormMixClusK | Normal mixture model estimation
NormMixParam | Calculate the mean and covariance for a Normal mixture model
plot | Visualize results from coseq clustering
plot-method | Visualize results from coseq clustering
plot-methods | Visualize results from coseq clustering
proba | Accessors for the assigned cluster labels of a coseqResults object.
proba-method | Accessors for the assigned cluster labels of a coseqResults object.
profiles | Accessors for the assigned cluster labels of a coseqResults object.
profiles-method | Accessors for the assigned cluster labels of a coseqResults object.
show | Accessors for the assigned cluster labels of a coseqResults object.
show-method | Accessors for the assigned cluster labels of a coseqResults object.
summary | Summarize results from coseq clustering
summary-method | Summarize results from coseq clustering
summary-methods | Summarize results from coseq clustering
tcounts | Accessors for the assigned cluster labels of a coseqResults object.
tcounts-method | Accessors for the assigned cluster labels of a coseqResults object.
transformationType | Accessors for the assigned cluster labels of a coseqResults object.
transformationType-method | Accessors for the assigned cluster labels of a coseqResults object.
transformRNAseq | Transform RNA-seq data using common transformations