mnem
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 yahoo.de>
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 | ||
NEWS | Text |
Details
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) (5.5 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_1.21.0.tar.gz |
Windows Binary (x86_64) | mnem_1.21.0.zip (64-bit only) |
macOS Binary (x86_64) | mnem_1.21.0.tgz |
macOS Binary (arm64) | mnem_1.21.0.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 |