:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-structstrings' .. highlight: bash bioconductor-structstrings ========================== .. conda:recipe:: bioconductor-structstrings :replaces_section_title: :noindex: Implementation of the dot bracket annotations with Biostrings :homepage: https://bioconductor.org/packages/3.18/bioc/html/Structstrings.html :license: Artistic-2.0 :recipe: /`bioconductor-structstrings `_/`meta.yaml `_ 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. .. conda:package:: bioconductor-structstrings |downloads_bioconductor-structstrings| |docker_bioconductor-structstrings| :versions: .. raw:: html
1.18.0-01.16.0-01.14.0-11.14.0-01.10.0-21.10.0-11.10.0-01.8.0-01.6.1-0 ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.10.0-2``,  ``1.10.0-1``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.1-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.3-0`` .. raw:: html
:depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocgenerics: ``>=0.48.1,<0.49.0a0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-biostrings: ``>=2.70.1,<2.71.0a0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-s4vectors: ``>=0.40.2,<0.41.0a0`` :depends bioconductor-xvector: ``>=0.42.0,<0.43.0`` :depends bioconductor-xvector: ``>=0.42.0,<0.43.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-crayon: :depends r-stringi: :depends r-stringr: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 quay.io/biocontainers/bioconductor-structstrings: (see `bioconductor-structstrings/tags`_ for valid values for ````) .. |downloads_bioconductor-structstrings| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-structstrings.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-structstrings :alt: (downloads) .. |docker_bioconductor-structstrings| image:: https://quay.io/repository/biocontainers/bioconductor-structstrings/status :target: https://quay.io/repository/biocontainers/bioconductor-structstrings .. _`bioconductor-structstrings/tags`: https://quay.io/repository/biocontainers/bioconductor-structstrings?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-structstrings/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-structstrings/README.html