:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-cummerbund' .. highlight: bash bioconductor-cummerbund ======================= .. conda:recipe:: bioconductor-cummerbund :replaces_section_title: :noindex: Analysis\, exploration\, manipulation\, and visualization of Cufflinks high\-throughput sequencing data. :homepage: https://bioconductor.org/packages/3.18/bioc/html/cummeRbund.html :license: Artistic-2.0 :recipe: /`bioconductor-cummerbund `_/`meta.yaml `_ :links: biotools: :biotools:`cummerbund`, doi: :doi:`10.1038/nprot.2012.016` Allows for persistent storage\, access\, exploration\, and manipulation of Cufflinks high\-throughput sequencing data. In addition\, provides numerous plotting functions for commonly used visualizations. .. conda:package:: bioconductor-cummerbund |downloads_bioconductor-cummerbund| |docker_bioconductor-cummerbund| :versions: .. raw:: html
2.44.0-02.42.0-02.40.0-02.36.0-02.34.0-02.32.0-12.32.0-02.30.0-02.28.0-0 ``2.44.0-0``,  ``2.42.0-0``,  ``2.40.0-0``,  ``2.36.0-0``,  ``2.34.0-0``,  ``2.32.0-1``,  ``2.32.0-0``,  ``2.30.0-0``,  ``2.28.0-0``,  ``2.26.0-1``,  ``2.24.0-0``,  ``2.22.0-0``,  ``2.20.0-0``,  ``2.18.0-0``,  ``2.16.0-0``,  ``2.12.1-1``,  ``2.12.1-0``,  ``2.8.2-1``,  ``2.8.2-0`` .. raw:: html
:depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-gviz: ``>=1.46.0,<1.47.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-fastcluster: :depends r-ggplot2: :depends r-plyr: :depends r-reshape2: :depends r-rsqlite: :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-cummerbund and update with:: mamba update bioconductor-cummerbund To create a new environment, run:: mamba create --name myenvname bioconductor-cummerbund 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-cummerbund: (see `bioconductor-cummerbund/tags`_ for valid values for ````) .. |downloads_bioconductor-cummerbund| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-cummerbund.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-cummerbund :alt: (downloads) .. |docker_bioconductor-cummerbund| image:: https://quay.io/repository/biocontainers/bioconductor-cummerbund/status :target: https://quay.io/repository/biocontainers/bioconductor-cummerbund .. _`bioconductor-cummerbund/tags`: https://quay.io/repository/biocontainers/bioconductor-cummerbund?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-cummerbund/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-cummerbund/README.html