netresponse: Functional Network Analysis

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Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling.

Author
Leo Lahti, Olli-Pekka Huovilainen, Antonio Gusmao and Juuso Parkkinen
Date of publication
None
Maintainer
Leo Lahti <leo.lahti@iki.fi>
License
GPL (>=2)
Version
1.34.0
URLs

View on Bioconductor

Man pages

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.matrix
check.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)
filter.netw
filter.netw
filter.network
filter.network
find.similar.features
Find similar features with a given subnetwork.
generate.toydata
generate.toydata
get.dat-NetResponseModel-method
Get subnetwork data
get.mis
get.mis
get.model.parameters
get.model.parameters
getqofz-NetResponseModel-method
Sample-to-response matrix of probabilities P(r|s).
get.subnets-NetResponseModel-method
get.subnets
ICMg.combined.sampler
ICMg.combined.sampler
ICMg.get.comp.memberships
ICMg.get.comp.memberships
ICMg.links.sampler
ICMg.links.sampler
independent.models
independent.models
listify.groupings
Convert grouping info into a list; each element corresponds...
list.responses.continuous.multi
Investigate association of a continuous variable and the...
list.responses.continuous.single
Investigate association of a continuous variable and the...
list.responses.factor
List significant responses
list.responses.factor.minimal
List factor responses (minimal)
list.significant.responses
Listing significant responses
mixture.model
Mixture model
model.stats
model.stats
NetResponseModel-class
Class "NetResponseModel"
netresponse-package
NetResponse: Global modeling of transcriptional responses in...
order.responses
order.responses
osmo
Osmoshock data set (PPI and expression)
pick.model.pairs
Pick model pairs
pick.model.parameters
pick.model.parameters
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.
PlotMixture
Plot mixtures
PlotMixtureBivariate
PlotMixtureBivariate
PlotMixtureMultivariate
PlotMixtureMultivariate
PlotMixtureMultivariate.deprecated
PlotMixtureMultivariate.deprecated
PlotMixtureUnivariate
Plot univariate mixtures
plotPCA
plotPCA
plot_response
plot_response
plot_responses
plot_responses
plot_scale
plot_scale
plot_subnet
plot_subnet
P.r.s
Description: Probabiity of mode given a sample (a data...
P.rS
Description: Probabiity of mode given multiple samples (ie....
P.rs.joint
Description: Joint probabiity density for mode and sample...
P.rs.joint.individual
Description: Joint probabiity density for mode and sample...
P.S
Description: Probabiity density for sample Mainly for...
P.s.individual
Description: Probabiity density for individual sample Mainly...
P.s.r
Description: Probabiity density for sample given mode Mainly...
P.Sr
Description: Probabiity density for sample group given mode...
read.sif
Reading network files
remove.negative.edges
remove.negative.edges
response2sample
response2sample
response.enrichment
Enrichment for a specified sample group in the given...
sample2response
sample2response
set.breaks
Set breaks
toydata
toydata
update.model.pair
update.model.pair
vdp.mixt
vdp.mixt
vectorize.groupings
Convert grouping info into a vector; each element corresponds...
write.netresponse.results
Write NetResponse results summary into a file.

Files in this package

netresponse/DESCRIPTION
netresponse/NAMESPACE
netresponse/R
netresponse/R/AllClasses.R
netresponse/R/AllGenerics.R
netresponse/R/ICMg.R
netresponse/R/ICMg.internals.R
netresponse/R/NetResponseModel-accessors.R
netresponse/R/PlotMixture.R
netresponse/R/PlotMixtureUnivariate.R
netresponse/R/add.ellipse.R
netresponse/R/bic.mixture.R
netresponse/R/bic.mixture.multivariate.R
netresponse/R/bic.mixture.univariate.R
netresponse/R/bic.select.best.mode.R
netresponse/R/check.matrix.R
netresponse/R/check.network.R
netresponse/R/continuous.responses.R
netresponse/R/deprecated.R
netresponse/R/detect.responses.R
netresponse/R/enrichment.list.R
netresponse/R/enrichment.list.factor.R
netresponse/R/enrichment.list.factor.minimal.R
netresponse/R/enrichment.score.R
netresponse/R/factor.responses.R
netresponse/R/factor.responses.minimal.R
netresponse/R/filter.netw.R
netresponse/R/firstlib.R
netresponse/R/get.mis.R
netresponse/R/independent.models.R
netresponse/R/information.criteria.R
netresponse/R/internals.R
netresponse/R/list.responses.continuous.R
netresponse/R/list.responses.continuous.multi.R
netresponse/R/list.responses.factor.R
netresponse/R/list.responses.factor.minimal.R
netresponse/R/listify.groupings.R
netresponse/R/mixture.densities.R
netresponse/R/mixture.model.R
netresponse/R/model.stats.R
netresponse/R/order.responses.R
netresponse/R/pick.model.pairs.R
netresponse/R/pick.model.parameters.R
netresponse/R/pkg-package.R
netresponse/R/plot-methods.R
netresponse/R/plot_matrix.R
netresponse/R/read.network.R
netresponse/R/response.enrichment.R
netresponse/R/response2sample.R
netresponse/R/sample2response.R
netresponse/R/show-methods.R
netresponse/R/toydata.R
netresponse/R/update.model.pair.R
netresponse/R/utilities.R
netresponse/R/vdp.mixt.R
netresponse/R/visualization.R
netresponse/README.md
netresponse/data
netresponse/data/dna.rda
netresponse/data/osmo.rda
netresponse/data/toydata.rda
netresponse/inst
netresponse/inst/CITATION
netresponse/inst/NEWS
netresponse/man
netresponse/man/ICMg.combined.sampler.Rd
netresponse/man/ICMg.get.comp.memberships.Rd
netresponse/man/ICMg.links.sampler.Rd
netresponse/man/NetResponseModel-class.Rd
netresponse/man/P.S.Rd
netresponse/man/P.Sr.Rd
netresponse/man/P.r.s.Rd
netresponse/man/P.rS.Rd
netresponse/man/P.rs.joint.Rd
netresponse/man/P.rs.joint.individual.Rd
netresponse/man/P.s.individual.Rd
netresponse/man/P.s.r.Rd
netresponse/man/PlotMixture.Rd
netresponse/man/PlotMixtureBivariate.Rd
netresponse/man/PlotMixtureMultivariate.Rd
netresponse/man/PlotMixtureMultivariate.deprecated.Rd
netresponse/man/PlotMixtureUnivariate.Rd
netresponse/man/add.ellipse.Rd
netresponse/man/bic.mixture.Rd
netresponse/man/bic.mixture.multivariate.Rd
netresponse/man/bic.mixture.univariate.Rd
netresponse/man/bic.select.best.mode.Rd
netresponse/man/centerData.Rd
netresponse/man/check.matrix.Rd
netresponse/man/check.network.Rd
netresponse/man/continuous.responses.Rd
netresponse/man/detect.responses.Rd
netresponse/man/dna.Rd
netresponse/man/enrichment.list.factor.Rd
netresponse/man/enrichment.list.factor.minimal.Rd
netresponse/man/factor.responses.Rd
netresponse/man/factor.responses.minimal.Rd
netresponse/man/filter.netw.Rd
netresponse/man/filter.network.Rd
netresponse/man/find.similar.features.Rd
netresponse/man/generate.toydata.Rd
netresponse/man/get.dat-NetResponseModel-method.Rd
netresponse/man/get.mis.Rd
netresponse/man/get.model.parameters.Rd
netresponse/man/get.subnets-NetResponseModel-method.Rd
netresponse/man/getqofz-NetResponseModel-method.Rd
netresponse/man/independent.models.Rd
netresponse/man/list.responses.continuous.multi.Rd
netresponse/man/list.responses.continuous.single.Rd
netresponse/man/list.responses.factor.Rd
netresponse/man/list.responses.factor.minimal.Rd
netresponse/man/list.significant.responses.Rd
netresponse/man/listify.groupings.Rd
netresponse/man/mixture.model.Rd
netresponse/man/model.stats.Rd
netresponse/man/netresponse-package.Rd
netresponse/man/order.responses.Rd
netresponse/man/osmo.Rd
netresponse/man/pick.model.pairs.Rd
netresponse/man/pick.model.parameters.Rd
netresponse/man/plotPCA.Rd
netresponse/man/plot_associations.Rd
netresponse/man/plot_data.Rd
netresponse/man/plot_expression.Rd
netresponse/man/plot_matrix.Rd
netresponse/man/plot_response.Rd
netresponse/man/plot_responses.Rd
netresponse/man/plot_scale.Rd
netresponse/man/plot_subnet.Rd
netresponse/man/read.sif.Rd
netresponse/man/remove.negative.edges.Rd
netresponse/man/response.enrichment.Rd
netresponse/man/response2sample.Rd
netresponse/man/sample2response.Rd
netresponse/man/set.breaks.Rd
netresponse/man/toydata.Rd
netresponse/man/update.model.pair.Rd
netresponse/man/vdp.mixt.Rd
netresponse/man/vectorize.groupings.Rd
netresponse/man/write.netresponse.results.Rd
netresponse/src
netresponse/src/Makevars
netresponse/src/netresponse.c
netresponse/tests
netresponse/tests/ICMg.test.R
netresponse/tests/bicmixture.R
netresponse/tests/mixture.model.test.R
netresponse/tests/mixture.model.test.multimodal.R
netresponse/tests/mixture.model.test.singlemode.R
netresponse/tests/timing.R
netresponse/tests/toydata2.R
netresponse/tests/validate.netresponse.R
netresponse/tests/validate.pca.basis.R
netresponse/tests/vdpmixture.R
netresponse/vignettes
netresponse/vignettes/NetResponse.Rmd
netresponse/vignettes/NetResponse.md
netresponse/vignettes/TODO
netresponse/vignettes/TODO/TODO.Rmd
netresponse/vignettes/fig
netresponse/vignettes/fig/NetResponse2-1.png
netresponse/vignettes/fig/NetResponse2b-1.png
netresponse/vignettes/fig/NetResponse3-1.png
netresponse/vignettes/fig/NetResponse4-1.png
netresponse/vignettes/fig/NetResponse5-1.png
netresponse/vignettes/fig/NetResponse7-1.png
netresponse/vignettes/fig/vdp-1.png
netresponse/vignettes/main.R
netresponse/vignettes/netresponse.bib
netresponse/vignettes/netresponse.pdf