:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-ballgown' .. highlight: bash bioconductor-ballgown ===================== .. conda:recipe:: bioconductor-ballgown :replaces_section_title: :noindex: Flexible\, isoform\-level differential expression analysis :homepage: https://bioconductor.org/packages/3.18/bioc/html/ballgown.html :license: Artistic-2.0 :recipe: /`bioconductor-ballgown `_/`meta.yaml `_ :links: biotools: :biotools:`ballgown`, doi: :doi:`10.1038/nbt.3172` Tools for statistical analysis of assembled transcriptomes\, including flexible differential expression analysis\, visualization of transcript structures\, and matching of assembled transcripts to annotation. .. conda:package:: bioconductor-ballgown |downloads_bioconductor-ballgown| |docker_bioconductor-ballgown| :versions: .. raw:: html
2.34.0-02.32.0-02.30.0-02.26.0-02.24.0-02.22.0-12.22.0-02.20.0-02.18.0-0 ``2.34.0-0``,  ``2.32.0-0``,  ``2.30.0-0``,  ``2.26.0-0``,  ``2.24.0-0``,  ``2.22.0-1``,  ``2.22.0-0``,  ``2.20.0-0``,  ``2.18.0-0``,  ``2.16.0-1``,  ``2.14.0-0``,  ``2.12.0-0``,  ``2.10.0-0``,  ``2.8.4-0``,  ``2.2.0-0`` .. raw:: html
:depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-sva: ``>=3.50.0,<3.51.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-rcolorbrewer: :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-ballgown and update with:: mamba update bioconductor-ballgown To create a new environment, run:: mamba create --name myenvname bioconductor-ballgown 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-ballgown: (see `bioconductor-ballgown/tags`_ for valid values for ````) .. |downloads_bioconductor-ballgown| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-ballgown.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-ballgown :alt: (downloads) .. |docker_bioconductor-ballgown| image:: https://quay.io/repository/biocontainers/bioconductor-ballgown/status :target: https://quay.io/repository/biocontainers/bioconductor-ballgown .. _`bioconductor-ballgown/tags`: https://quay.io/repository/biocontainers/bioconductor-ballgown?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-ballgown/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-ballgown/README.html