:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-rsubread' .. highlight: bash bioconductor-rsubread ===================== .. conda:recipe:: bioconductor-rsubread :replaces_section_title: :noindex: Mapping\, quantification and variant analysis of sequencing data :homepage: https://bioconductor.org/packages/3.17/bioc/html/Rsubread.html :license: GPL (>=3) :recipe: /`bioconductor-rsubread `_/`meta.yaml `_ :links: biotools: :biotools:`rsubread` Alignment\, quantification and analysis of RNA sequencing data \(including both bulk RNA\-seq and scRNA\-seq\) and DNA sequenicng data \(including ATAC\-seq\, ChIP\-seq\, WGS\, WES etc\). Includes functionality for read mapping\, read counting\, SNP calling\, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads. .. conda:package:: bioconductor-rsubread |downloads_bioconductor-rsubread| |docker_bioconductor-rsubread| :versions: .. raw:: html
2.16.0-02.14.2-02.12.0-12.12.0-02.8.2-02.8.1-02.8.0-02.6.1-02.4.3-0 ``2.16.0-0``,  ``2.14.2-0``,  ``2.12.0-1``,  ``2.12.0-0``,  ``2.8.2-0``,  ``2.8.1-0``,  ``2.8.0-0``,  ``2.6.1-0``,  ``2.4.3-0``,  ``2.4.0-0``,  ``2.2.1-0``,  ``2.0.0-0``,  ``1.34.6-0``,  ``1.34.4-0``,  ``1.34.0-0``,  ``1.32.4-0``,  ``1.32.2-0``,  ``1.30.9-0``,  ``1.28.1-0``,  ``1.28.0-0``,  ``1.26.1-0``,  ``1.25.2-0``,  ``1.23.0-0``,  ``1.22.1-0`` .. raw:: html
: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-matrix: :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-rsubread and update with:: mamba update bioconductor-rsubread To create a new environment, run:: mamba create --name myenvname bioconductor-rsubread 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-rsubread: (see `bioconductor-rsubread/tags`_ for valid values for ````) .. |downloads_bioconductor-rsubread| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-rsubread.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-rsubread :alt: (downloads) .. |docker_bioconductor-rsubread| image:: https://quay.io/repository/biocontainers/bioconductor-rsubread/status :target: https://quay.io/repository/biocontainers/bioconductor-rsubread .. _`bioconductor-rsubread/tags`: https://quay.io/repository/biocontainers/bioconductor-rsubread?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-rsubread/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-rsubread/README.html