netresponse: Functional Network Analysis

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

AuthorLeo Lahti, Olli-Pekka Huovilainen, Antonio Gusmao and Juuso Parkkinen
Date of publicationNone
MaintainerLeo Lahti <leo.lahti@iki.fi>
LicenseGPL (>=2)
Version1.34.0
https://github.com/antagomir/netresponse

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

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