mnem

DOI: 10.18129/B9.bioc.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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF	R Script	mnem
PDF		Reference Manual
Text		NEWS

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) (< 6 months)
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
LinkingTo	Rcpp, RcppEigen
Suggests	knitr, devtools, rmarkdown, BiocGenerics, RUnit
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
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
Package Short Url	https://bioconductor.org/packages/mnem/
Package Downloads Report	Download Stats