:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-granulator' .. highlight: bash bioconductor-granulator ======================= .. conda:recipe:: bioconductor-granulator :replaces_section_title: :noindex: Rapid benchmarking of methods for \*in silico\* deconvolution of bulk RNA\-seq data :homepage: https://bioconductor.org/packages/3.18/bioc/html/granulator.html :license: GPL-3 :recipe: /`bioconductor-granulator `_/`meta.yaml `_ granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA\-seq data or single cell RNA\-seq expression profiles. The package provides a unified testing interface to rapidly run and benchmark multiple state\-of\-the\-art deconvolution methods. Data for the deconvolution of peripheral blood mononuclear cells \(PBMCs\) into individual immune cell types is provided as well. .. conda:package:: bioconductor-granulator |downloads_bioconductor-granulator| |docker_bioconductor-granulator| :versions: ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.2.0-0``,  ``1.0.0-0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-cowplot: :depends r-dplyr: :depends r-dtangle: :depends r-e1071: :depends r-epir: :depends r-ggplot2: :depends r-ggplotify: :depends r-limsolve: :depends r-magrittr: :depends r-mass: :depends r-nnls: :depends r-pheatmap: :depends r-purrr: :depends r-rlang: :depends r-tibble: :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-granulator and update with:: mamba update bioconductor-granulator To create a new environment, run:: mamba create --name myenvname bioconductor-granulator 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-granulator: (see `bioconductor-granulator/tags`_ for valid values for ````) .. |downloads_bioconductor-granulator| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-granulator.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-granulator :alt: (downloads) .. |docker_bioconductor-granulator| image:: https://quay.io/repository/biocontainers/bioconductor-granulator/status :target: https://quay.io/repository/biocontainers/bioconductor-granulator .. _`bioconductor-granulator/tags`: https://quay.io/repository/biocontainers/bioconductor-granulator?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-granulator/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-granulator/README.html