Introduction | Loading epiNEM | Quick start | Simulations | Yeast knock-out screens | Identification of significant modulators for pairs of double knock-outs | Validation of identified interactions | String-db interactions | Graph based GO similarity scores | Enrichment analysis | Enrichment of identified sets of modulators for each double knock-out | Enrichment of effect reporters for each identified modulator | Creation of data objects | Session information | References
Package: epiNEM 1.37.0
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:
epiNEM_1.37.0.tar.gz
epiNEM_1.37.0.zip(r-4.7)epiNEM_1.37.0.zip(r-4.6)epiNEM_1.37.0.zip(r-4.5)
epiNEM_1.37.0.tgz(r-4.6-any)epiNEM_1.37.0.tgz(r-4.5-any)
epiNEM_1.37.0.tar.gz(r-4.7-any)epiNEM_1.37.0.tar.gz(r-4.6-any)
epiNEM_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
epiNEM/json (API)
| # Install 'epiNEM' in R: |
| install.packages('epiNEM', repos = c('https://bioc.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
Last updated from:30ccf2565e. Checks:1 FAILURE, 7 NOTE, 1 ERROR, 1 OK. Indexed: yes.
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| bioc-checks | FAILURE | 229 | ||
| linux-devel-x86_64 | NOTE | 366 | ||
| source / vignettes | ERROR | 378 | ||
| linux-release-x86_64 | NOTE | 357 | ||
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| macos-oldrel-arm64 | NOTE | 197 | ||
| windows-devel | NOTE | 237 | ||
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| windows-oldrel | NOTE | 230 | ||
| wasm-release | OK | 222 |
Exports:AddLogicGatesCreateExtendedAdjacencyCreateRandomGraphCreateTopologyepiAnnoepiNEMepiScreenExtendTopologyGenerateDataHeatmapOPMllperm.rank.testrank.enrichmentSimEpiNEM
Dependencies:abindamapapclusterbdsmatrixBHBiocGenericsBiocManagerBoolNetBoutrosLab.plotting.generalclasscliclueclustercolorspacecorpcorcpp11data.tabledeldirDEoptimRdipteste1071ellipsefarverfastclusterfastICAflexclustflexmixfpcgdatagenericsggdendroggmggplot2gluegmodelsgraphgridExtragtablegtoolshexbinigraphinfotheointerpisobandjpegkernlablabelinglatex2explatticelatticeExtralifecyclelimmaLinnormlmtestmagrittrMASSMatrixmatrixStatsmclustmgcvminetmnemmodeltoolsnaturalsortnlmennetpcalgpermutepkgconfigpngprabclusproxyR6RBGLRColorBrewerRcppRcppArmadilloRcppEigenRgraphvizrlangrobustbaseRtsneS7scalessfsmiscsnowsnowfallstatmodtsnevcdvctrsveganviridisLitewesandersonwithrXMLzoo
Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.
| Epistatic Nested Effects Models: | Inferring mixed epistasis from indirect measurements of knock-out screens
Last update: 2021-02-15
Started: 2017-03-04
