:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-fission' .. highlight: bash bioconductor-fission ==================== .. conda:recipe:: bioconductor-fission :replaces_section_title: :noindex: RangedSummarizedExperiment for time course RNA\-Seq of fission yeast in response to stress\, by Leong et al.\, Nat Commun 2014. :homepage: https://bioconductor.org/packages/3.18/data/experiment/html/fission.html :license: LGPL :recipe: /`bioconductor-fission `_/`meta.yaml `_ This package provides a RangedSummarizedExperiment object of read counts in genes for a time course RNA\-Seq experiment of fission yeast \(Schizosaccharomyces pombe\) in response to oxidative stress \(1M sorbitol treatment\) at 0\, 15\, 30\, 60\, 120 and 180 mins. The samples are further divided between a wild\-type group and a group with deletion of atf21. The read count matrix was prepared and provided by the author of the study\: Leong HS\, Dawson K\, Wirth C\, Li Y\, Connolly Y\, Smith DL\, Wilkinson CR\, Miller CJ. \"A global non\-coding RNA system modulates fission yeast protein levels in response to stress\". Nat Commun 2014 May 23\;5\:3947. PMID\: 24853205. GEO\: GSE56761. .. conda:package:: bioconductor-fission |downloads_bioconductor-fission| |docker_bioconductor-fission| :versions: .. raw:: html
1.22.0-01.20.0-01.18.0-01.14.0-11.14.0-01.12.0-01.10.0-11.10.0-01.8.0-0 ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-1``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.2.0-0`` .. raw:: html
:depends bioconductor-data-packages: ``>=20231203`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :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-fission and update with:: mamba update bioconductor-fission To create a new environment, run:: mamba create --name myenvname bioconductor-fission 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-fission: (see `bioconductor-fission/tags`_ for valid values for ````) .. |downloads_bioconductor-fission| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-fission.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-fission :alt: (downloads) .. |docker_bioconductor-fission| image:: https://quay.io/repository/biocontainers/bioconductor-fission/status :target: https://quay.io/repository/biocontainers/bioconductor-fission .. _`bioconductor-fission/tags`: https://quay.io/repository/biocontainers/bioconductor-fission?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-fission/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-fission/README.html