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.

Functions

add.ellipse Man page
bic.mixture Man page
bic.mixture.multivariate Man page
bic.mixture.univariate Man page
bic.select.best.mode Man page
centerData Man page
check.matrix Man page
check.network Man page
continuous.responses Man page
detect.responses Man page
dna Man page
enrichment.list.factor Man page
enrichment.list.factor.minimal Man page
factor.responses Man page
factor.responses.minimal Man page
filter.netw Man page
filter.network Man page
find.similar.features Man page
generate.toydata Man page
get.dat Man page
get.dat,NetResponseModel-method Man page
get.mis Man page
get.model.parameters Man page
getqofz Man page
getqofz,NetResponseModel-method Man page
get.subnets Man page
get.subnets,NetResponseModel-method Man page
ICMg.combined.sampler Man page
ICMg.get.comp.memberships Man page
ICMg.links.sampler Man page
independent.models Man page
listify.groupings Man page
list.responses.continuous.multi Man page
list.responses.continuous.single Man page
list.responses.factor Man page
list.responses.factor.minimal Man page
list.significant.responses Man page
mixture.model Man page
model.stats Man page
netresponse Man page
NetResponseModel-class Man page
[[,NetResponseModel-method Man page
netresponse-package Man page
order.responses Man page
osmo Man page
pick.model.pairs Man page
pick.model.parameters Man page
plot_associations Man page
plot_data Man page
plot_expression Man page
plot_matrix Man page
PlotMixture Man page
PlotMixtureBivariate Man page
PlotMixtureMultivariate Man page
PlotMixtureMultivariate.deprecated Man page
PlotMixtureUnivariate Man page
plotPCA Man page
plot_response Man page
plot_responses Man page
plot_scale Man page
plot_subnet Man page
P.r.s Man page
P.rS Man page
P.rs.joint Man page
P.rs.joint.individual Man page
P.S Man page
P.s.individual Man page
P.s.r Man page
P.Sr Man page
read.sif Man page
remove.negative.edges Man page
response2sample Man page
response.enrichment Man page
sample2response Man page
set.breaks Man page
show,NetResponseModel-method Man page
toydata Man page
update.model.pair Man page
vdp.mixt Man page
vectorize.groupings Man page
write.netresponse.results Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.