recipe bioconductor-target

Predict Combined Function of Transcription Factors






Implement the BETA algorithm for infering direct target genes from DNA-binding and perturbation expression data Wang et al. (2013) <doi: 10.1038/nprot.2013.150>. Extend the algorithm to predict the combined function of two DNA-binding elements from comprable binding and expression data.

package bioconductor-target

(downloads) docker_bioconductor-target



depends bioconductor-biocgenerics:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends r-base:


depends r-matrixstats:

depends r-shiny:



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-target

and update with::

   mamba update bioconductor-target

To create a new environment, run:

mamba create --name myenvname bioconductor-target

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-target/tags`_ for valid values for ``<tag>``)

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