:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-toast' .. highlight: bash bioconductor-toast ================== .. conda:recipe:: bioconductor-toast :replaces_section_title: :noindex: Tools for the analysis of heterogeneous tissues :homepage: https://bioconductor.org/packages/3.18/bioc/html/TOAST.html :license: GPL-2 :recipe: /`bioconductor-toast `_/`meta.yaml `_ This package is devoted to analyzing high\-throughput data \(e.g. gene expression microarray\, DNA methylation microarray\, RNA\-seq\) from complex tissues. Current functionalities include 1. detect cell\-type specific or cross\-cell type differential signals 2. tree\-based differential analysis 3. improve variable selection in reference\-free deconvolution 4. partial reference\-free deconvolution with prior knowledge. .. conda:package:: bioconductor-toast |downloads_bioconductor-toast| |docker_bioconductor-toast| :versions: ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.7.1-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-0`` :depends bioconductor-epidish: ``>=2.18.0,<2.19.0`` :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-corpcor: :depends r-doparallel: :depends r-ggally: :depends r-ggplot2: :depends r-nnls: :depends r-quadprog: :depends r-tidyr: :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-toast and update with:: mamba update bioconductor-toast To create a new environment, run:: mamba create --name myenvname bioconductor-toast 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-toast: (see `bioconductor-toast/tags`_ for valid values for ````) .. |downloads_bioconductor-toast| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-toast.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-toast :alt: (downloads) .. |docker_bioconductor-toast| image:: https://quay.io/repository/biocontainers/bioconductor-toast/status :target: https://quay.io/repository/biocontainers/bioconductor-toast .. _`bioconductor-toast/tags`: https://quay.io/repository/biocontainers/bioconductor-toast?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-toast/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-toast/README.html