:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-saturn' .. highlight: bash bioconductor-saturn =================== .. conda:recipe:: bioconductor-saturn :replaces_section_title: :noindex: Scalable Analysis of Differential Transcript Usage for Bulk and Single\-Cell RNA\-sequencing Applications :homepage: https://bioconductor.org/packages/3.18/bioc/html/satuRn.html :license: Artistic-2.0 :recipe: /`bioconductor-saturn `_/`meta.yaml `_ satuRn provides a higly performant and scalable framework for performing differential transcript usage analyses. The package consists of three main functions. The first function\, fitDTU\, fits quasi\-binomial generalized linear models that model transcript usage in different groups of interest. The second function\, testDTU\, tests for differential usage of transcripts between groups of interest. Finally\, plotDTU visualizes the usage profiles of transcripts in groups of interest. .. conda:package:: bioconductor-saturn |downloads_bioconductor-saturn| |docker_bioconductor-saturn| :versions: ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.2.0-0``,  ``1.0.0-0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-boot: :depends r-ggplot2: :depends r-locfdr: :depends r-matrix: :depends r-pbapply: :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-saturn and update with:: mamba update bioconductor-saturn To create a new environment, run:: mamba create --name myenvname bioconductor-saturn 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-saturn: (see `bioconductor-saturn/tags`_ for valid values for ````) .. |downloads_bioconductor-saturn| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-saturn.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-saturn :alt: (downloads) .. |docker_bioconductor-saturn| image:: https://quay.io/repository/biocontainers/bioconductor-saturn/status :target: https://quay.io/repository/biocontainers/bioconductor-saturn .. _`bioconductor-saturn/tags`: https://quay.io/repository/biocontainers/bioconductor-saturn?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-saturn/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-saturn/README.html