nempi

DOI: 10.18129/B9.bioc.nempi  

Inferring unobserved perturbations from gene expression data

Bioconductor version: Release (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 yahoo.de>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	nempi
PDF		Reference Manual
Text		NEWS

Details

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
LinkingTo
Suggests	knitr, BiocGenerics, rmarkdown, RUnit
SystemRequirements
Enhances
URL	https://github.com/cbg-ethz/nempi/
BugReports	https://github.com/cbg-ethz/nempi/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	nempi_1.6.0.tar.gz
Windows Binary	nempi_1.6.0.zip
macOS Binary (x86_64)	nempi_1.6.0.tgz
macOS Binary (arm64)	nempi_1.6.0.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