mnem
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see mnem.
Mixture Nested Effects Models
Bioconductor version: 3.9
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
Maintainer: Martin Pirkl <martin.pirkl at bsse.ethz.ch>
citation("mnem")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, CRISPR, DNASeq, GeneExpression, Network, NetworkInference, Pathways, PooledScreens, RNASeq, SingleCell, Software, SystemsBiology |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| License | GPL-3 |
| Depends | R (>= 3.6) |
| Imports | cluster, nem, epiNEM, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices |
| System Requirements | |
| URL |
See More
| Suggests | knitr, devtools, rmarkdown, BiocGenerics, RUnit |
| Linking To | Rcpp, RcppEigen |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| 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_1.0.0.tar.gz |
| Windows Binary | mnem_1.0.0.zip |
| Mac OS X 10.11 (El Capitan) | mnem_1.0.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |