Package: mnem
Type: Package
Title: Mixture Nested Effects Models
Version: 1.27.0
Authors@R: person("Martin", "Pirkl", email = "martinpirkl@yahoo.de",role = c("aut", "cre"))
Description: 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.
Depends: R (>= 4.1)
License: GPL-3
Encoding: UTF-8
LazyData: true
biocViews: Pathways, SystemsBiology, NetworkInference, Network, RNASeq,
        PooledScreens, SingleCell, CRISPR, ATACSeq, DNASeq,
        GeneExpression
RoxygenNote: 7.3.2
Imports: cluster, graph, Rgraphviz, flexclust, lattice, naturalsort,
        snowfall, stats4, tsne, methods, graphics, stats, utils,
        Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices,
        e1071, ggplot2, wesanderson
LinkingTo: Rcpp, RcppEigen
VignetteBuilder: knitr
Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM,
        BiocStyle
NeedsCompilation: yes
BugReports: https://github.com/cbg-ethz/mnem/issues
URL: https://github.com/cbg-ethz/mnem/
Config/pak/sysreqs: libglpk-dev libxml2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:52:33 UTC
RemoteUrl: https://github.com/bioc/mnem
RemoteRef: HEAD
RemoteSha: 0fd323ed948bda54f931b3eba9ed34ccc95ff389
Packaged: 2026-02-03 09:42:30 UTC; root
Author: Martin Pirkl [aut, cre]
Maintainer: Martin Pirkl <martinpirkl@yahoo.de>
Built: R 4.6.0; x86_64-apple-darwin20; 2026-02-03 09:54:47 UTC; unix
