:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-spicyr' .. highlight: bash bioconductor-spicyr =================== .. conda:recipe:: bioconductor-spicyr :replaces_section_title: :noindex: Spatial analysis of in situ cytometry data :homepage: https://bioconductor.org/packages/3.18/bioc/html/spicyR.html :license: GPL (>=2) :recipe: /`bioconductor-spicyr `_/`meta.yaml `_ The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell\-resolution spatial omics technologies. spicyR consists of three primary steps\: \(i\) summarizing the degree of spatial localization between pairs of cell types for each image\; \(ii\) modelling the variability in localization summary statistics as a function of cell counts and \(iii\) testing for changes in spatial localizations associated with a response variable. .. conda:package:: bioconductor-spicyr |downloads_bioconductor-spicyr| |docker_bioconductor-spicyr| :versions: ``1.14.2-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.1-0``,  ``1.2.0-0``,  ``1.0.0-0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-classifyr: ``>=3.6.0,<3.7.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-singlecellexperiment: ``>=1.24.0,<1.25.0`` :depends bioconductor-spatialexperiment: ``>=1.12.0,<1.13.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-concaveman: :depends r-data.table: :depends r-dplyr: :depends r-ggforce: :depends r-ggplot2: :depends r-lmertest: :depends r-mgcv: :depends r-pheatmap: :depends r-rlang: :depends r-scam: :depends r-spatstat.explore: :depends r-spatstat.geom: :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-spicyr and update with:: mamba update bioconductor-spicyr To create a new environment, run:: mamba create --name myenvname bioconductor-spicyr 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-spicyr: (see `bioconductor-spicyr/tags`_ for valid values for ````) .. |downloads_bioconductor-spicyr| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-spicyr.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-spicyr :alt: (downloads) .. |docker_bioconductor-spicyr| image:: https://quay.io/repository/biocontainers/bioconductor-spicyr/status :target: https://quay.io/repository/biocontainers/bioconductor-spicyr .. _`bioconductor-spicyr/tags`: https://quay.io/repository/biocontainers/bioconductor-spicyr?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-spicyr/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-spicyr/README.html