recipe bioconductor-statial

A package to identify changes in cell state relative to spatial associations

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/Statial.html

License:

GPL-3

Recipe:

/bioconductor-statial/meta.yaml

Statial is a suite of functions for identifying changes in cell state. The functionality provided by Statial provides robust quantification of cell type localisation which are invariant to changes in tissue structure. In addition to this Statial uncovers changes in marker expression associated with varying levels of localisation. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with.

package bioconductor-statial

versions:

1.4.5-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

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-ggplot2:

depends r-magrittr:

depends r-plotly:

depends r-purrr:

depends r-ranger:

depends r-spatstat.explore:

depends r-spatstat.geom:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

depends r-tidyselect:

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-statial

and update with::

   mamba update bioconductor-statial

To create a new environment, run:

mamba create --name myenvname bioconductor-statial

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-statial:<tag>

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

Download stats

Link to this page

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