recipe bioconductor-dce

Pathway Enrichment Based on Differential Causal Effects






Compute differential causal effects (dce) on (biological) networks. Given observational samples from a control experiment and non-control (e.g., cancer) for two genes A and B, we can compute differential causal effects with a (generalized) linear regression. If the causal effect of gene A on gene B in the control samples is different from the causal effect in the non-control samples the dce will differ from zero. We regularize the dce computation by the inclusion of prior network information from pathway databases such as KEGG.

package bioconductor-dce

(downloads) docker_bioconductor-dce



depends bioconductor-edger:


depends bioconductor-epinem:


depends bioconductor-graph:


depends bioconductor-graphite:


depends bioconductor-mnem:




depends bioconductor-rgraphviz:


depends r-assertthat:

depends r-base:


depends r-dplyr:

depends r-expm:

depends r-ggplot2:

depends r-ggraph:

depends r-glm2:

depends r-glue:

depends r-harmonicmeanp:

depends r-igraph:

depends r-logger:

depends r-magrittr:

depends r-mass:

depends r-matrix:

depends r-metap:

depends r-naturalsort:

depends r-pcalg:

depends r-ppcor:

depends r-purrr:

depends r-reshape2:

depends r-rlang:

depends r-shadowtext:

depends r-tidygraph:

depends r-tidyverse:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-dce

and update with::

   mamba update bioconductor-dce

To create a new environment, run:

mamba create --name myenvname bioconductor-dce

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-dce/tags`_ for valid values for ``<tag>``)

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