recipe bioconductor-spasim

Spatial point data simulator for tissue images

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-spasim/meta.yaml

A suite of functions for simulating spatial patterns of cells in tissue images. Output images are multitype point data in SingleCellExperiment format. Each point represents a cell, with its 2D locations and cell type. Potential cell patterns include background cells, tumour/immune cell clusters, immune rings, and blood/lymphatic vessels.

package bioconductor-spasim

(downloads) docker_bioconductor-spasim

versions:

1.4.0-0,  1.2.1-0,  1.0.0-0

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-dplyr:

depends r-ggplot2:

depends r-rann:

depends r-spatstat.geom:

depends r-spatstat.random:

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-spasim

and update with::

   mamba update bioconductor-spasim

To create a new environment, run:

mamba create --name myenvname bioconductor-spasim

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-spasim:<tag>

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

Download stats

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-spasim/README.html)