recipe bioconductor-spicyr

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.

package 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:

Installation

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-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:<tag>

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

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Link to this page

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