recipe bioconductor-nearbynding

Discern RNA structure proximal to protein binding






Provides a pipeline to discern RNA structure at and proximal to the site of protein binding within regions of the transcriptome defined by the user. CLIP protein-binding data can be input as either aligned BAM or peak-called bedGraph files. RNA structure can either be predicted internally from sequence or users have the option to input their own RNA structure data. RNA structure binding profiles can be visually and quantitatively compared across multiple formats.

package bioconductor-nearbynding

(downloads) docker_bioconductor-nearbynding



depends bioconductor-biocgenerics:


depends bioconductor-genomeinfodb:


depends bioconductor-genomicranges:


depends bioconductor-plyranges:


depends bioconductor-rsamtools:


depends bioconductor-rtracklayer:


depends bioconductor-s4vectors:


depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:


depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene:


depends r-base:


depends r-dplyr:

depends r-ggplot2:

depends r-gplots:

depends r-magrittr:

depends r-matrixstats:

depends r-r.utils:

depends r-rlang:

depends r-transport:



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-nearbynding

and update with::

   mamba update bioconductor-nearbynding

To create a new environment, run:

mamba create --name myenvname bioconductor-nearbynding

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

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