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Bioconductor - nempi

nempi

This is the released version of nempi; for the devel version, see nempi.

Inferring unobserved perturbations from gene expression data

Bioconductor version: Release (3.21)

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 yahoo.de>

Citation (from within R, enter citation("nempi")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("nempi")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("nempi")
Details biocViews ATACSeq, CRISPR, Classification, DNASeq, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneSignaling, Network, NetworkInference, NeuralNetwork, Pathways, PooledScreens, RNASeq, SingleCell, Software, SystemsBiology Version 1.16.0 In Bioconductor since BioC 3.13 (R-4.1) (4 years) License GPL-3 Depends R (>= 4.1), mnem Imports e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats, epiNEM System Requirements URL https://github.com/cbg-ethz/nempi/ Bug Reports https://github.com/cbg-ethz/nempi/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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