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

Mixture Nested Effects Models

Bioconductor version: Development (3.20)

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>

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


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

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


To view documentation for the version of this package installed in your system, start R and enter:

mnem HTML R Script
Reference Manual PDF


biocViews ATACSeq, CRISPR, DNASeq, GeneExpression, Network, NetworkInference, Pathways, PooledScreens, RNASeq, SingleCell, Software, SystemsBiology
Version 1.21.0
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
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Suggests knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle
Linking To Rcpp, RcppEigen
Depends On Me nempi
Imports Me bnem, dce, epiNEM
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Source Package mnem_1.21.0.tar.gz
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