:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-fscanr' .. highlight: bash bioconductor-fscanr =================== .. conda:recipe:: bioconductor-fscanr :replaces_section_title: :noindex: Detect Programmed Ribosomal Frameshifting Events from mRNA\/cDNA BLASTX Output :homepage: https://bioconductor.org/packages/3.17/bioc/html/FScanR.html :license: Artistic-2.0 :recipe: /`bioconductor-fscanr `_/`meta.yaml `_ \'FScanR\' identifies Programmed Ribosomal Frameshifting \(PRF\) events from BLASTX homolog sequence alignment between targeted genomic\/cDNA\/mRNA sequences against the peptide library of the same species or a close relative. The output by BLASTX or diamond BLASTX will be used as input of \'FScanR\' and should be in a tabular format with 14 columns. For BLASTX\, the output parameter should be\: \-outfmt \'6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qframe sframe\'. For diamond BLASTX\, the output parameter should be\: \-outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qframe qframe. .. conda:package:: bioconductor-fscanr |downloads_bioconductor-fscanr| |docker_bioconductor-fscanr| :versions: ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-2``,  ``1.0.0-1`` :depends r-base: ``>=4.3,<4.4.0a0`` :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-fscanr and update with:: mamba update bioconductor-fscanr To create a new environment, run:: mamba create --name myenvname bioconductor-fscanr 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-fscanr: (see `bioconductor-fscanr/tags`_ for valid values for ````) .. |downloads_bioconductor-fscanr| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-fscanr.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-fscanr :alt: (downloads) .. |docker_bioconductor-fscanr| image:: https://quay.io/repository/biocontainers/bioconductor-fscanr/status :target: https://quay.io/repository/biocontainers/bioconductor-fscanr .. _`bioconductor-fscanr/tags`: https://quay.io/repository/biocontainers/bioconductor-fscanr?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-fscanr/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-fscanr/README.html