:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-bsgenome.drerio.ucsc.danrer5.masked' .. highlight: bash bioconductor-bsgenome.drerio.ucsc.danrer5.masked ================================================ .. conda:recipe:: bioconductor-bsgenome.drerio.ucsc.danrer5.masked :replaces_section_title: :noindex: Full masked genome sequences for Danio rerio \(UCSC version danRer5\) :homepage: https://bioconductor.org/packages/3.18/data/annotation/html/BSgenome.Drerio.UCSC.danRer5.masked.html :license: Artistic-2.0 :recipe: /`bioconductor-bsgenome.drerio.ucsc.danrer5.masked `_/`meta.yaml `_ Full genome sequences for Danio rerio \(Zebrafish\) as provided by UCSC \(danRer5\, Jul. 2007\) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer5\, except that each of them has the 4 following masks on top\: \(1\) the mask of assembly gaps \(AGAPS mask\)\, \(2\) the mask of intra\-contig ambiguities \(AMB mask\)\, \(3\) the mask of repeats from RepeatMasker \(RM mask\)\, and \(4\) the mask of repeats from Tandem Repeats Finder \(TRF mask\). Only the AGAPS and AMB masks are \"active\" by default. .. conda:package:: bioconductor-bsgenome.drerio.ucsc.danrer5.masked |downloads_bioconductor-bsgenome.drerio.ucsc.danrer5.masked| |docker_bioconductor-bsgenome.drerio.ucsc.danrer5.masked| :versions: .. raw:: html
1.3.99-121.3.99-111.3.99-101.3.99-91.3.99-81.3.99-71.3.99-61.3.99-51.3.99-4 ``1.3.99-12``,  ``1.3.99-11``,  ``1.3.99-10``,  ``1.3.99-9``,  ``1.3.99-8``,  ``1.3.99-7``,  ``1.3.99-6``,  ``1.3.99-5``,  ``1.3.99-4``,  ``1.3.99-3``,  ``1.3.99-2``,  ``1.3.99-0`` .. raw:: html
:depends bioconductor-bsgenome: ``>=1.70.0,<1.71.0`` :depends bioconductor-bsgenome.drerio.ucsc.danrer5: ``>=1.4.0,<1.5.0`` :depends bioconductor-data-packages: ``>=20231203`` :depends curl: :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-bsgenome.drerio.ucsc.danrer5.masked and update with:: mamba update bioconductor-bsgenome.drerio.ucsc.danrer5.masked To create a new environment, run:: mamba create --name myenvname bioconductor-bsgenome.drerio.ucsc.danrer5.masked 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-bsgenome.drerio.ucsc.danrer5.masked: (see `bioconductor-bsgenome.drerio.ucsc.danrer5.masked/tags`_ for valid values for ````) .. |downloads_bioconductor-bsgenome.drerio.ucsc.danrer5.masked| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-bsgenome.drerio.ucsc.danrer5.masked.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-bsgenome.drerio.ucsc.danrer5.masked :alt: (downloads) .. |docker_bioconductor-bsgenome.drerio.ucsc.danrer5.masked| image:: https://quay.io/repository/biocontainers/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/status :target: https://quay.io/repository/biocontainers/bioconductor-bsgenome.drerio.ucsc.danrer5.masked .. _`bioconductor-bsgenome.drerio.ucsc.danrer5.masked/tags`: https://quay.io/repository/biocontainers/bioconductor-bsgenome.drerio.ucsc.danrer5.masked?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-bsgenome.drerio.ucsc.danrer5.masked/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-bsgenome.drerio.ucsc.danrer5.masked/README.html