DESCRIPTION

Package: mnem
Type: Package
Title: Mixture Nested Effects Models
Version: 1.23.0
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/