Package: netresponse 1.67.0

Leo Lahti

netresponse: Functional Network Analysis

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

Authors:Leo Lahti, Olli-Pekka Huovilainen, Antonio Gusmao and Juuso Parkkinen

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netresponse.pdf |netresponse.html✨
netresponse/json (API)
NEWS

# Install 'netresponse' in R:
install.packages('netresponse', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/antagomir/netresponse/issues

Datasets:

On BioConductor:netresponse-1.65.0(bioc 3.20)netresponse-1.64.0(bioc 3.19)

cellbiologyclusteringgeneexpressiongeneticsnetworkgraphandnetworkdifferentialexpressionmicroarraynetworkinferencetranscription

5.64 score 3 stars 21 scripts 245 downloads 26 exports 66 dependencies

Last updated 23 days agofrom:71a1a40be4. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-win-x86_64NOTEOct 30 2024
R-4.5-linux-x86_64NOTEOct 30 2024
R-4.4-win-x86_64NOTEOct 30 2024
R-4.4-mac-x86_64NOTEOct 30 2024
R-4.4-mac-aarch64NOTEOct 30 2024
R-4.3-win-x86_64NOTEOct 30 2024
R-4.3-mac-x86_64NOTEOct 30 2024
R-4.3-mac-aarch64NOTEOct 30 2024

Exports:centerDatacontinuous.responsesdetect.responsesenrichment.list.factor.minimalfactor.responsesfactor.responses.minimalfind.similar.featuresgenerate.toydataget.model.parametersget.subnetsindependent.modelslist.responses.continuous.multilist.responses.continuous.singlelistify.groupingsmixture.modelmodel.statsorder.responsespick.model.parametersplot_matrixplot_responseplot_responsesplot_subnetresponse2samplesample2responseset.breaksvdp.mixt

Dependencies:base64encBiocGenericsBiocManagerBiocStylebookdownbslibcachemclicolorspacecpp11digestevaluatefansifarverfastmapfontawesomefsggplot2gluegraphgtablehighrhtmltoolsigraphinfotheoisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmclustmemoisemgcvmimeminetmunsellnlmepillarpkgconfigplyrqvalueR6rappdirsRColorBrewerRcppreshape2Rgraphvizrlangrmarkdownsassscalesstringistringrtibbletinytexutf8vctrsviridisLitewithrxfunyaml

Introduction to the netresponse R package

Leo Lahti et al.

Rendered fromNetResponse.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-03-27
Started: 2014-10-27

Readme and manuals

Help Manual

Help pageTopics
NetResponse: Global modeling of transcriptional responses in interaction networksnetresponse-package netresponse
Add ellipse to an existing plotadd.ellipse
BIC mixturebic.mixture
Multivariate BIC mixturebic.mixture.multivariate
Univariate BIC mixturebic.mixture.univariate
Select best mode with BICbic.select.best.mode
Center data matrix.centerData
check.networkcheck.network
Continuous responsescontinuous.responses
detect.responsesdetect.responses
Dna damage data set (PPI and expression)dna
enrichment.list.factorenrichment.list.factor
enrichment.list.factorenrichment.list.factor.minimal
Factor responsesfactor.responses
Factor responses (minimal)factor.responses.minimal
Find similar features with a given subnetwork.find.similar.features
Get subnetwork dataget.dat get.dat,NetResponseModel-method
get.misget.mis
get.model.parametersget.model.parameters
get.subnetsget.subnets get.subnets,NetResponseModel-method
Investigate association of a continuous variable and the modeslist.responses.continuous.multi
Investigate association of a continuous variable and the modeslist.responses.continuous.single
List significant responseslist.responses.factor
List factor responses (minimal)list.responses.factor.minimal
Listing significant responseslist.significant.responses
Convert grouping info into a list; each element corresponds to a group and lists samples in that group.listify.groupings
Mixture modelmixture.model
model.statsmodel.stats
Class 'NetResponseModel'NetResponseModel-class show,NetResponseModel-method [[,NetResponseModel-method
order.responsesorder.responses
Osmoshock data set (PPI and expression)osmo
Association strength between category labels and responses.plot_associations
Plot observed data.plot_data
plot_expressionplot_expression
Visualize a matrix with one or two-way color scale.plot_matrix
plot_responseplot_response
plot_responsesplot_responses
plot_scaleplot_scale
plot_subnetplot_subnet
Plot mixturesPlotMixture
PlotMixtureBivariatePlotMixtureBivariate
PlotMixtureMultivariatePlotMixtureMultivariate
Plot univariate mixturesPlotMixtureUnivariate
plotPCAplotPCA
Reading network filesread.sif
Enrichment for a specified sample group in the given response.response.enrichment
response2sampleresponse2sample
sample2responsesample2response
Set breaksset.breaks
split.qofzsplit.qofz
toydatatoydata
vdp.mixtvdp.mixt
Convert grouping info into a vector; each element corresponds to a group and lists samples in that group.vectorize.groupings
Write NetResponse results summary into a file.write.netresponse.results