DOI: 10.18129/B9.bioc.nempi  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see nempi.

Inferring unobserved perturbations from gene expression data

Bioconductor version: 3.16

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.

Author: Martin Pirkl [aut, cre]

Maintainer: Martin Pirkl <martinpirkl at>

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biocViews ATACSeq, CRISPR, Classification, DNASeq, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneSignaling, Network, NetworkInference, NeuralNetwork, Pathways, PooledScreens, RNASeq, SingleCell, Software, SystemsBiology
Version 1.6.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License GPL-3
Depends R (>= 4.1), mnem
Imports e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats, epiNEM
Suggests knitr, BiocGenerics, rmarkdown, RUnit
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