:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-recount3' .. highlight: bash bioconductor-recount3 ===================== .. conda:recipe:: bioconductor-recount3 :replaces_section_title: :noindex: Explore and download data from the recount3 project :homepage: https://bioconductor.org/packages/3.18/bioc/html/recount3.html :license: Artistic-2.0 :recipe: /`bioconductor-recount3 `_/`meta.yaml `_ The recount3 package enables access to a large amount of uniformly processed RNA\-seq data from human and mouse. You can download RangedSummarizedExperiment objects at the gene\, exon or exon\-exon junctions level with sample metadata and QC statistics. In addition we provide access to sample coverage BigWig files. .. conda:package:: bioconductor-recount3 |downloads_bioconductor-recount3| |docker_bioconductor-recount3| :versions: ``1.12.0-0``,  ``1.10.2-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.1-0``,  ``1.0.7-0``,  ``1.0.0-1`` :depends bioconductor-biocfilecache: ``>=2.10.0,<2.11.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-data.table: :depends r-httr: :depends r-matrix: :depends r-r.utils: :depends r-sessioninfo: :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-recount3 and update with:: mamba update bioconductor-recount3 To create a new environment, run:: mamba create --name myenvname bioconductor-recount3 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-recount3: (see `bioconductor-recount3/tags`_ for valid values for ````) .. |downloads_bioconductor-recount3| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-recount3.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-recount3 :alt: (downloads) .. |docker_bioconductor-recount3| image:: https://quay.io/repository/biocontainers/bioconductor-recount3/status :target: https://quay.io/repository/biocontainers/bioconductor-recount3 .. _`bioconductor-recount3/tags`: https://quay.io/repository/biocontainers/bioconductor-recount3?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-recount3/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-recount3/README.html