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 199 downloads 4 exports 105 dependencies

Last updated 4 months agofrom:f9f289f6c4. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 28 2025
R-4.5-winOKJan 28 2025
R-4.5-macOKJan 28 2025
R-4.5-linuxOKJan 28 2025
R-4.4-winOKJan 28 2025
R-4.4-macOKJan 28 2025
R-4.3-winOKJan 28 2025
R-4.3-macOKJan 28 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 Jan 28 2025.

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