Package: netresponse 1.73.0

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

# Install 'netresponse' in R:

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

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

Datasets:

dna - Dna damage data set
osmo - Osmoshock data set
toydata - Toydata

On BioConductor:netresponse-1.73.0(bioc 3.24)netresponse-1.72.0(bioc 3.23)

cellbiology clustering geneexpression genetics network graphandnetwork differentialexpression microarray networkinference transcription

5.84 score 3 stars 33 scripts 26 exports 59 dependencies

Last updated from:8072ad4948. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	158
linux-devel-arm64	NOTE	206
linux-devel-x86_64	NOTE	227
source / vignettes	OK	203
linux-release-arm64	NOTE	183
linux-release-x86_64	NOTE	195
macos-release-arm64	NOTE	131
macos-release-x86_64	NOTE	207
macos-oldrel-arm64	NOTE	143
macos-oldrel-x86_64	NOTE	255
windows-devel	NOTE	125
windows-release	NOTE	134
windows-oldrel	NOTE	148
wasm-release	OK	151

Exports:centerData continuous.responses detect.responses enrichment.list.factor.minimal factor.responses factor.responses.minimal find.similar.features generate.toydata get.model.parameters get.subnets independent.models list.responses.continuous.multi list.responses.continuous.single listify.groupings mixture.model model.stats order.responses pick.model.parameters plot_matrix plot_response plot_responses plot_subnet response2sample sample2response set.breaks vdp.mixt

Dependencies:base64enc BiocGenerics BiocManager BiocStyle bookdown bslib cachem cli cpp11 digest evaluate farver fastmap fontawesome fs generics ggplot2 glue graph gtable highr htmltools igraph infotheo isoband jquerylib jsonlite knitr labeling lattice lifecycle magrittr Matrix mclust memoise mime minet pkgconfig plyr qvalue R6 rappdirs RColorBrewer Rcpp reshape2 Rgraphviz rlang rmarkdown S7 sass scales stringi stringr tinytex vctrs viridisLite withr xfun yaml

Introduction to the netresponse R package

Rendered fromNetResponse.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

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