recipe bioconductor-structstrings

Implementation of the dot bracket annotations with Biostrings






The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.

package bioconductor-structstrings

(downloads) docker_bioconductor-structstrings



depends bioconductor-biocgenerics:


depends bioconductor-biocgenerics:


depends bioconductor-biostrings:


depends bioconductor-biostrings:


depends bioconductor-iranges:


depends bioconductor-iranges:


depends bioconductor-s4vectors:


depends bioconductor-s4vectors:


depends bioconductor-xvector:


depends bioconductor-xvector:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends r-base:


depends r-crayon:

depends r-stringi:

depends r-stringr:



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-structstrings

and update with::

   mamba update bioconductor-structstrings

To create a new environment, run:

mamba create --name myenvname bioconductor-structstrings

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

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