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nempi

This is the development version of nempi; for the stable release version, see nempi.

Inferring unobserved perturbations from gene expression data

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("nempi")

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

Documentation

Reference Manual PDF

Details

biocViews ATACSeq, CRISPR, Classification, DNASeq, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneSignaling, Network, NetworkInference, NeuralNetwork, Pathways, PooledScreens, RNASeq, SingleCell, Software, SystemsBiology
Version 1.9.0
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
Linking To
Suggests knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle
System Requirements
Enhances
URL https://github.com/cbg-ethz/nempi/
Bug Reports https://github.com/cbg-ethz/nempi/issues
See More
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Build Report  

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64) nempi_1.9.0.tgz
macOS Binary (arm64) nempi_1.9.0.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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