recipe bioconductor-spiat

Spatial Image Analysis of Tissues



Artistic-2.0 + file LICENSE



SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.

package bioconductor-spiat

(downloads) docker_bioconductor-spiat



depends bioconductor-dittoseq:


depends bioconductor-spatialexperiment:


depends bioconductor-summarizedexperiment:


depends r-apcluster:


depends r-base:


depends r-dbscan:


depends r-dplyr:


depends r-ggplot2:


depends r-gridextra:


depends r-gtools:


depends r-mmand:


depends r-pracma:


depends r-rann:


depends r-raster:

depends r-reshape2:


depends r-rlang:

depends r-sp:

depends r-spatstat.explore:

depends r-spatstat.geom:

depends r-tibble:


depends r-vroom:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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-spiat

and update with::

   mamba update bioconductor-spiat

To create a new environment, run:

mamba create --name myenvname bioconductor-spiat

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<tag>

(see `bioconductor-spiat/tags`_ for valid values for ``<tag>``)

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