add.ellipse             Add ellipse to an existing plot
bic.mixture             BIC mixture
bic.mixture.multivariate
                        Multivariate BIC mixture
bic.mixture.univariate
                        Univariate BIC mixture
bic.select.best.mode    Select best mode with BIC
centerData              Center data matrix.
check.network           check.network
continuous.responses    Continuous responses
detect.responses        detect.responses
dna                     Dna damage data set (PPI and expression)
enrichment.list.factor
                        enrichment.list.factor
enrichment.list.factor.minimal
                        enrichment.list.factor
factor.responses        Factor responses
factor.responses.minimal
                        Factor responses (minimal)
find.similar.features   Find similar features with a given subnetwork.
get.dat,NetResponseModel-method
                        Get subnetwork data
get.mis                 get.mis
get.model.parameters    get.model.parameters
get.subnets,NetResponseModel-method
                        get.subnets
list.responses.continuous.multi
                        Investigate association of a continuous
                        variable and the modes
list.responses.continuous.single
                        Investigate association of a continuous
                        variable and the modes
list.responses.factor   List significant responses
list.responses.factor.minimal
                        List factor responses (minimal)
list.significant.responses
                        Listing significant responses
listify.groupings       Convert grouping info into a list; each element
                        corresponds to a group and lists samples in
                        that group.
mixture.model           Mixture model
model.stats             model.stats
netresponse-package     NetResponse: Global modeling of transcriptional
                        responses in interaction networks
NetResponseModel-class
                        Class 'NetResponseModel'
order.responses         order.responses
osmo                    Osmoshock data set (PPI and expression)
plot_associations       Association strength between category labels
                        and responses.
plot_data               Plot observed data.
plot_expression         plot_expression
plot_matrix             Visualize a matrix with one or two-way color
                        scale.
plot_response           plot_response
plot_responses          plot_responses
plot_scale              plot_scale
plot_subnet             plot_subnet
PlotMixture             Plot mixtures
PlotMixtureBivariate    PlotMixtureBivariate
PlotMixtureMultivariate
                        PlotMixtureMultivariate
PlotMixtureUnivariate   Plot univariate mixtures
plotPCA                 plotPCA
read.sif                Reading network files
response.enrichment     Enrichment for a specified sample group in the
                        given response.
response2sample         response2sample
sample2response         sample2response
set.breaks              Set breaks
split.qofz              split.qofz
toydata                 toydata
vdp.mixt                vdp.mixt
vectorize.groupings     Convert grouping info into a vector; each
                        element corresponds to a group and lists
                        samples in that group.
write.netresponse.results
                        Write NetResponse results summary into a file.
