mnem
Mixture Nested Effects Models
Bioconductor version: Release (3.17)
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 "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.16.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (4.5 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 |
| Linking To | Rcpp, RcppEigen |
| Suggests | knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle |
| System Requirements | |
| Enhances | |
| URL | https://github.com/cbg-ethz/mnem/ |
| Bug Reports | https://github.com/cbg-ethz/mnem/issues |
See More
| Depends On Me | nempi |
| Imports Me | bnem, dce, epiNEM |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | mnem_1.16.0.tar.gz |
| Windows Binary | mnem_1.16.0.zip |
| macOS Binary (x86_64) | mnem_1.16.0.tgz |
| macOS Binary (arm64) | mnem_1.16.0.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 |