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 |