nempi

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see nempi.

Inferring unobserved perturbations from gene expression data

Bioconductor version: 3.20

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 "4.4") 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")

nempi HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ATACSeq, CRISPR, Classification, DNASeq, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneSignaling, Network, NetworkInference, NeuralNetwork, Pathways, PooledScreens, RNASeq, SingleCell, Software, SystemsBiology

Version 1.14.0

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

Suggests knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle

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Package Archives

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

Source Package nempi_1.14.0.tar.gz

Windows Binary (x86_64) nempi_1.14.0.zip

macOS Binary (x86_64) nempi_1.14.0.tgz

macOS Binary (arm64) nempi_1.14.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/nempi

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/nempi

Bioc Package Browser https://code.bioconductor.org/browse/nempi/

Package Short Url https://bioconductor.org/packages/nempi/

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