recipe bioconductor-bindingsitefinder

Binding site defintion based on iCLIP data






Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette.

package bioconductor-bindingsitefinder

(downloads) docker_bioconductor-bindingsitefinder



depends bioconductor-complexheatmap:


depends bioconductor-genomeinfodb:


depends bioconductor-genomicfeatures:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-rtracklayer:


depends bioconductor-s4vectors:


depends r-base:


depends r-dplyr:

depends r-forcats:

depends r-ggdist:

depends r-ggforce:

depends r-ggplot2:

depends r-kableextra:

depends r-lifecycle:

depends r-matrixstats:

depends r-plyr:

depends r-rcolorbrewer:

depends r-rlang:

depends r-tibble:

depends r-tidyr:



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-bindingsitefinder

and update with::

   mamba update bioconductor-bindingsitefinder

To create a new environment, run:

mamba create --name myenvname bioconductor-bindingsitefinder

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

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