Package: nempi 1.15.0

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]

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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-1.15.0(bioc 3.21)nempi-1.14.0(bioc 3.20)

softwaregeneexpressiondifferentialexpressiondifferentialmethylationgenesignalingpathwaysnetworkclassificationneuralnetworknetworkinferenceatacseqdnaseqrnaseqpooledscreenscrisprsinglecellsystemsbiology

4.60 score 2 stars 2 scripts 226 downloads 4 exports 105 dependencies

Last updated 5 months agofrom:f9f289f6c4. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 29 2025
R-4.5-winOKMar 29 2025
R-4.5-macOKMar 29 2025
R-4.5-linuxOKMar 29 2025
R-4.4-winOKMar 29 2025
R-4.4-macOKMar 29 2025
R-4.4-linuxOKMar 29 2025
R-4.3-winOKMar 29 2025
R-4.3-macOKMar 29 2025

Exports:classpinempinempibspifit

Dependencies:abindamapapclusterbdsmatrixBHBiocGenericsBiocManagerBoolNetBoutrosLab.plotting.generalclasscliclueclustercolorspacecorpcorcpp11data.tabledeldirDEoptimRdipteste1071ellipseepiNEMfansifarverfastclusterfastICAflexclustflexmixfpcgdatagenericsggdendroggmggplot2gluegmodelsgraphgridExtragtablegtoolshexbinigraphinfotheointerpisobandjpegkernlablabelinglatex2explatticelatticeExtralifecyclelimmaLinnormlmtestmagrittrMASSMatrixmatrixStatsmclustmgcvminetmnemmodeltoolsmunsellnaturalsortnlmennetpcalgpermutepillarpkgconfigpngprabclusproxyR6randomForestRBGLRColorBrewerRcppRcppArmadilloRcppEigenRgraphvizrlangrobustbaseRtsnescalessfsmiscsnowsnowfallstatmodstringistringrtibbletsneutf8vcdvctrsveganviridisLitewesandersonwithrXMLzoo

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

Martin Pirkl, Niko Beerenwinkel

Rendered fromnempi.Rmdusingknitr::rmarkdownon Mar 29 2025.

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