Package: epiNEM 1.36.0

Martin Pirkl

epiNEM: epiNEM

epiNEM is an extension of the original Nested Effects Models (NEM). EpiNEM is able to take into account double knockouts and infer more complex network signalling pathways. It is tailored towards large scale double knock-out screens.

Authors:Madeline Diekmann & Martin Pirkl

epiNEM_1.36.0.tar.gz
epiNEM_1.36.0.zip(r-4.7)epiNEM_1.36.0.zip(r-4.6)epiNEM_1.36.0.zip(r-4.5)
epiNEM_1.36.0.tgz(r-4.6-any)epiNEM_1.36.0.tgz(r-4.5-any)
epiNEM_1.36.0.tar.gz(r-4.7-any)epiNEM_1.36.0.tar.gz(r-4.6-any)
epiNEM_1.36.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
epiNEM/json (API)
NEWS

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

Bug tracker:https://github.com/cbg-ethz/epinem/issues

Datasets:
  • sameith_GO - Graph-based GO similarity scores, string GO annotations for Sameith et al., 2015 data
  • sameith_string - Sig. of string interaction scores for Sameith et al., 2015 data
  • samscreen - Example data: epiNEM results for the Sameith et al., 2015 knock-out screen
  • sim - Example data: simulation results
  • wageningen_GO - Graph-based GO similarity scores, string GO annotations for van Wageningen et al., 2015 data
  • wageningen_string - Sig. of string interaction scores for van Wageningen et al., 2010 data
  • wagscreen - Example data: epiNEM results for the Wageningen et al., 2010 knock-out screen "http://www.holstegelab.nl/publications/GSTF_geneticinteractions/ downloads/del_mutants_limma.txt"

On BioConductor:epiNEM-1.37.0(bioc 3.24)epiNEM-1.36.0(bioc 3.23)

pathwayssystemsbiologynetworkinferencenetwork

5.48 score 1 stars 2 packages 3 scripts 444 downloads 1 mentions 14 exports 97 dependencies

Last updated from:73fc1eea40 (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 1 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING273
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source / vignettesERROR361
linux-release-x86_64NOTE419
macos-release-arm64NOTE188
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wasm-releaseOK249

Exports:AddLogicGatesCreateExtendedAdjacencyCreateRandomGraphCreateTopologyepiAnnoepiNEMepiScreenExtendTopologyGenerateDataHeatmapOPMllperm.rank.testrank.enrichmentSimEpiNEM

Dependencies:abindamapapclusterbdsmatrixBHBiocGenericsBiocManagerBoolNetBoutrosLab.plotting.generalclasscliclueclustercolorspacecorpcorcpp11data.tabledeldirDEoptimRdipteste1071ellipsefarverfastclusterfastICAflexclustflexmixfpcgdatagenericsggdendroggmggplot2gluegmodelsgraphgridExtragtablegtoolshexbinigraphinfotheointerpisobandjpegkernlablabelinglatex2explatticelatticeExtralifecyclelimmaLinnormlmtestmagrittrMASSMatrixmatrixStatsmclustmgcvminetmnemmodeltoolsnaturalsortnlmennetpcalgpermutepkgconfigpngprabclusproxyR6RBGLRColorBrewerRcppRcppArmadilloRcppEigenRgraphvizrlangrobustbaseRtsneS7scalessfsmiscsnowsnowfallstatmodtsnevcdvctrsveganviridisLitewesandersonwithrXMLzoo

| Epistatic Nested Effects Models: | Inferring mixed epistasis from indirect measurements of knock-out screens

Martin Pirkl, Madeline Diekmann, Marlies van der Wees, Niko Beerenwinkel, Holger Fröhlich, Florian Markowetz

Rendered fromepiNEM.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-02-15
Started: 2017-03-04