recipe bioconductor-mnem

Mixture Nested Effects Models

Homepage:

https://bioconductor.org/packages/3.14/bioc/html/mnem.html

License:

GPL-3

Recipe:

/bioconductor-mnem/meta.yaml

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.

package bioconductor-mnem

Versions:

1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.5-0,  1.6.1-0,  1.4.0-0

Depends:

• bioconductor-graph >=1.72.0,<1.73.0

• bioconductor-linnorm >=2.18.0,<2.19.0

• bioconductor-rgraphviz >=2.38.0,<2.39.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=10.3.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=10.3.0

• r-base >=4.1,<4.2.0a0

• r-cluster

• r-data.table

• r-e1071

• r-flexclust

• r-ggplot2

• r-lattice

• r-matrixstats

• r-naturalsort

• r-rcpp

• r-rcppeigen

• r-snowfall

• r-tsne

• r-wesanderson

Required By:

• bioconductor-dce

• bioconductor-bnem

• bioconductor-epinem

• bioconductor-nempi

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-mnem

and update with:

conda update bioconductor-mnem

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-mnem:<tag>

(see bioconductor-mnem/tags for valid values for <tag>)

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