Package: epiNEM 1.31.0

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_1.31.0.tar.gz
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epiNEM.pdf |epiNEM.html✨
epiNEM/json (API)
NEWS

# 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-1.31.0(bioc 3.21)epiNEM-1.30.0(bioc 3.20)

pathways systemsbiology networkinference network

5.83 score 1 stars 3 packages 1 scripts 326 downloads 1 mentions 14 exports 103 dependencies

Last updated 4 months agofrom:6d6ef3ad0b. Checks:1 ERROR, 7 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	FAIL	Jan 28 2025
R-4.5-win	NOTE	Jan 28 2025
R-4.5-mac	NOTE	Jan 28 2025
R-4.5-linux	NOTE	Jan 28 2025
R-4.4-win	NOTE	Jan 28 2025
R-4.4-mac	NOTE	Jan 28 2025
R-4.3-win	NOTE	Jan 28 2025
R-4.3-mac	NOTE	Jan 28 2025

Exports:AddLogicGates CreateExtendedAdjacency CreateRandomGraph CreateTopology epiAnno epiNEM epiScreen ExtendTopology GenerateData HeatmapOP Mll perm.rank.test rank.enrichment SimEpiNEM

Dependencies:abind amap apcluster bdsmatrix BH BiocGenerics BiocManager BoolNet BoutrosLab.plotting.general class cli clue cluster colorspace corpcor cpp11 data.table deldir DEoptimR diptest e1071 ellipse fansi farver fastcluster fastICA flexclust flexmix fpc gdata generics ggdendro ggm ggplot2 glue gmodels graph gridExtra gtable gtools hexbin igraph infotheo interp isoband jpeg kernlab labeling latex2exp lattice latticeExtra lifecycle limma Linnorm lmtest magrittr MASS Matrix matrixStats mclust mgcv minet mnem modeltools munsell naturalsort nlme nnet pcalg permute pillar pkgconfig png prabclus proxy R6 RBGL RColorBrewer Rcpp RcppArmadillo RcppEigen Rgraphviz rlang robustbase Rtsne scales sfsmisc snow snowfall statmod stringi stringr tibble tsne utf8 vcd vctrs vegan viridisLite wesanderson withr XML zoo

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

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

Rendered fromepiNEM.Rmdusingknitr::rmarkdownon Jan 28 2025.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add logic.	AddLogicGates
Create an extended adjacency matrix	CreateExtendedAdjacency
Create a random graph	CreateRandomGraph
Create Topology.	CreateTopology
Gate visualisation.	epiAnno
Epistatic NEMs - main function.	epiNEM
Analyse large double knock-out screen.	epiScreen
Extending topology of normal "nem"	ExtendTopology
Generate data from extended model.	GenerateData
Heatmap.	HeatmapOP
Evaluation of graphs	Mll
AUC permutation test	perm.rank.test
Plot pathway.	plot.epiNEM
Plot screen.	plot.epiScreen
Plot simulations.	plot.epiSim
Rank enrichment	rank.enrichment
graph-based GO similarity scores, string GO annotations for Sameith et al., 2015 data	sameith_GO
sig. of string interaction scores for Sameith et al., 2015 data	sameith_string
Example data: epiNEM results for the Sameith et al., 2015 knock-out screen	samscreen
Example data: simulation results	sim
Compare algorithms.	SimEpiNEM
graph-based GO similarity scores, string GO annotations for van Wageningen et al., 2015 data	wageningen_GO
sig. of string interaction scores for van Wageningen et al., 2010 data	wageningen_string
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"	wagscreen