Package: nempi 1.21.0

Martin Pirkl

nempi: Inferring unobserved perturbations from gene expression data

Takes as input an incomplete perturbation profile and differential gene expression in log odds and infers unobserved perturbations and augments observed ones. The inference is done by iteratively inferring a network from the perturbations and inferring perturbations from the network. The network inference is done by Nested Effects Models.

Authors:Martin Pirkl [aut, cre]

nempi_1.21.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
nempi/json (API)
NEWS

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

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

On BioConductor:nempi-1.21.0(bioc 3.24)nempi-1.20.0(bioc 3.23)

softwaregeneexpressiondifferentialexpressiondifferentialmethylationgenesignalingpathwaysnetworkclassificationneuralnetworknetworkinferenceatacseqdnaseqrnaseqpooledscreenscrisprsinglecellsystemsbiology

4.60 score 2 stars 4 scripts 330 downloads 4 exports 99 dependencies

Last updated from:99206de282. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING223
linux-devel-x86_64OK296
source / vignettesOK284
linux-release-x86_64OK317
macos-release-arm64OK171
macos-oldrel-arm64OK130
windows-develOK177
windows-releaseOK232
windows-oldrelOK184
wasm-releaseOK203

Exports:classpinempinempibspifit

Dependencies:abindamapapclusterbdsmatrixBHBiocGenericsBiocManagerBoolNetBoutrosLab.plotting.generalclasscliclueclustercolorspacecorpcorcpp11data.tabledeldirDEoptimRdipteste1071ellipseepiNEMfarverfastclusterfastICAflexclustflexmixfpcgdatagenericsggdendroggmggplot2gluegmodelsgraphgridExtragtablegtoolshexbinigraphinfotheointerpisobandjpegkernlablabelinglatex2explatticelatticeExtralifecyclelimmaLinnormlmtestmagrittrMASSMatrixmatrixStatsmclustmgcvminetmnemmodeltoolsnaturalsortnlmennetpcalgpermutepkgconfigpngprabclusproxyR6randomForestRBGLRColorBrewerRcppRcppArmadilloRcppEigenRgraphvizrlangrobustbaseRtsneS7scalessfsmiscsnowsnowfallstatmodtsnevcdvctrsveganviridisLitewesandersonwithrXMLzoo

| Nested Effects Models-based perturbation inference: | Inference of unobserved perturbations from gene expression profiles.

Martin Pirkl, Niko Beerenwinkel

Rendered fromnempi.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2022-09-23
Started: 2019-09-02