Package: CNORfeeder 1.45.0

Attila Gabor

CNORfeeder: Integration of CellNOptR to add missing links

This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with links derived from the data via various inference methods and uses information on physical interactions of proteins to guide and validate the integration of links.

Authors:Federica Eduati [aut], Enio Gjerga [ctb], Attila Gabor [cre]

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

# Install 'CNORfeeder' in R:

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

Datasets:

PPINigraph - Protein-protein interaction netwrok
UniprotIDdream - Uniprot identifiers for proteins in DreamModel
cnolist - CNOlist
cnolist - CNOlist
database - OmniPath PPI
feederObject - Feeder Object
indices - Mis-fit indices
integratedModel - Integrated Model
model - Prior Knowledge Network
model - Prior Knowledge Network
simData - CNORode simuation data

On BioConductor:CNORfeeder-1.45.0(bioc 3.20)CNORfeeder-1.44.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

12 exports 1.69 score 62 dependencies 2 mentions

Last updated 2 months agofrom:49fc8d1393

Exports:Binference buildFeederObjectDynamic gaBinaryT1W identifyMisfitIndices integrateLinks linksRanking makeBTables mapBTables2model mapDDN2model MIinference runDynamicFeeder weighting

Dependencies:base64enc BH BiocGenerics bitops bslib cachem CellNOptR cli colorspace cpp11 digest evaluate fansi farver fastmap fontawesome fs ggplot2 glue graph gtable highr htmltools igraph isoband jquerylib jsonlite knitr labeling lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme pillar pkgconfig R6 rappdirs RBGL RColorBrewer RCurl Rgraphviz rlang rmarkdown sass scales stringi stringr tibble tinytex utf8 vctrs viridisLite withr xfun XML yaml

Main vignette:Playing with networks using CNORfeeder

Rendered fromCNORfeeder-vignette.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2023-02-09
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
R package to integrate literature-constrained and data-driven methods to infer signalling networks from perturbation experiments	CNORfeeder-package CNORfeeder
Bayesian network inference	Binference
Building Feeder-Object for the integration to the PKN	buildFeederObjectDynamic
CNOlist	cnolist
OmniPath PPI	database
Feeder Object	feederObject
Genetic algorithm used to optimise a model differently weighting links	gaBinaryT1W
Identifying indices of poorly fitted measurements	identifyMisfitIndices
Mis-fit indices	indices
Integrated Model	integratedModel
Integrating the new links to the PKN	integrateLinks
Ranking of links inferred from data	linksRanking
Make Boolean tables	makeBTables
Integrate Boolean tables with the model	mapBTables2model
Integrate data-drive network with the model	mapDDN2model
Mutual information based network inference	MIinference
Prior Knowledge Network	model
Protein-protein interaction netwrok	PPINigraph
Modelling the integrated PKN with CNORode	runDynamicFeeder
CNORode simuation data	simData
Uniprot identifiers for proteins in DreamModel	UniprotIDdream
Weight integrated links.	weighting