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nempi

Inferring unobserved perturbations from gene expression data


Bioconductor version: Release (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")

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

Details

biocViews ATACSeq, CRISPR, Classification, DNASeq, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneSignaling, Network, NetworkInference, NeuralNetwork, Pathways, PooledScreens, RNASeq, SingleCell, Software, SystemsBiology
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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
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_1.10.0.tar.gz
Windows Binary nempi_1.10.0.zip (64-bit only)
macOS Binary (x86_64) nempi_1.10.0.tgz
macOS Binary (arm64) nempi_1.10.0.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/
Package Downloads Report Download Stats