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mnem

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

Mixture Nested Effects Models


Bioconductor version: Development (3.19)

Mixture Nested Effects Models (mnem) is an extension of Nested Effects Models and allows for the analysis of single cell perturbation data provided by methods like Perturb-Seq (Dixit et al., 2016) or Crop-Seq (Datlinger et al., 2017). In those experiments each of many cells is perturbed by a knock-down of a specific gene, i.e. several cells are perturbed by a knock-down of gene A, several by a knock-down of gene B, ... and so forth. The observed read-out has to be multi-trait and in the case of the Perturb-/Crop-Seq gene are expression profiles for each cell. mnem uses a mixture model to simultaneously cluster the cell population into k clusters and and infer k networks causally linking the perturbed genes for each cluster. The mixture components are inferred via an expectation maximization algorithm.

Author: Martin Pirkl [aut, cre]

Maintainer: Martin Pirkl <martinpirkl at yahoo.de>

Citation (from within R, enter citation("mnem")):

Installation

To install this package, start R (version "4.4") and enter:


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

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

BiocManager::install("mnem")

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("mnem")
mnem HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ATACSeq, CRISPR, DNASeq, GeneExpression, Network, NetworkInference, Pathways, PooledScreens, RNASeq, SingleCell, Software, SystemsBiology
Version 1.19.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL-3
Depends R (>= 4.1)
Imports cluster, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices, e1071, ggplot2, wesanderson
System Requirements
URL https://github.com/cbg-ethz/mnem/
Bug Reports https://github.com/cbg-ethz/mnem/issues
See More
Suggests knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle
Linking To Rcpp, RcppEigen
Enhances
Depends On Me nempi
Imports Me bnem, dce, epiNEM
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package mnem_1.19.0.tar.gz
Windows Binary mnem_1.19.0.zip
macOS Binary (x86_64) mnem_1.19.0.tgz
macOS Binary (arm64) mnem_1.19.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/mnem
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/mnem
Bioc Package Browser https://code.bioconductor.org/browse/mnem/
Package Short Url https://bioconductor.org/packages/mnem/
Package Downloads Report Download Stats