:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-recount' .. highlight: bash bioconductor-recount ==================== .. conda:recipe:: bioconductor-recount :replaces_section_title: :noindex: Explore and download data from the recount project :homepage: https://bioconductor.org/packages/3.14/bioc/html/recount.html :license: Artistic-2.0 :recipe: /`bioconductor-recount `_/`meta.yaml `_ Explore and download data from the recount project available at https\:\/\/jhubiostatistics.shinyapps.io\/recount\/. Using the recount package you can download RangedSummarizedExperiment objects at the gene\, exon or exon\-exon junctions level\, the raw counts\, the phenotype metadata used\, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http\:\/\/bioconductor.org\/packages\/derfinder you can perform annotation\-agnostic differential expression analyses with the data from the recount project as described at http\:\/\/www.nature.com\/nbt\/journal\/v35\/n4\/full\/nbt.3838.html. .. conda:package:: bioconductor-recount |downloads_bioconductor-recount| |docker_bioconductor-recount| :versions: .. raw:: html
1.20.0-01.18.0-01.16.1-01.16.0-01.14.0-01.12.0-01.10.8-01.8.1-01.6.3-0 ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.1-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.8-0``,  ``1.8.1-0``,  ``1.6.3-0``,  ``1.4.5-0``,  ``1.4.0-0`` .. raw:: html
:depends bioconductor-biocparallel: ``>=1.28.0,<1.29.0`` :depends bioconductor-derfinder: ``>=1.28.0,<1.29.0`` :depends bioconductor-genomeinfodb: ``>=1.30.0,<1.31.0`` :depends bioconductor-genomicranges: ``>=1.46.0,<1.47.0`` :depends bioconductor-geoquery: ``>=2.62.0,<2.63.0`` :depends bioconductor-iranges: ``>=2.28.0,<2.29.0`` :depends bioconductor-rtracklayer: ``>=1.54.0,<1.55.0`` :depends bioconductor-s4vectors: ``>=0.32.0,<0.33.0`` :depends bioconductor-summarizedexperiment: ``>=1.24.0,<1.25.0`` :depends r-base: ``>=4.1,<4.2.0a0`` :depends r-downloader: :depends r-rcurl: :depends r-rentrez: :requirements: .. rubric:: Installation With an activated Bioconda channel (see :ref:`set-up-channels`), install with:: conda install bioconductor-recount and update with:: conda update bioconductor-recount or use the docker container:: docker pull quay.io/biocontainers/bioconductor-recount: (see `bioconductor-recount/tags`_ for valid values for ````) .. |downloads_bioconductor-recount| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-recount.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-recount :alt: (downloads) .. |docker_bioconductor-recount| image:: https://quay.io/repository/biocontainers/bioconductor-recount/status :target: https://quay.io/repository/biocontainers/bioconductor-recount .. _`bioconductor-recount/tags`: https://quay.io/repository/biocontainers/bioconductor-recount?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-recount/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-recount/README.html