recipe bioconductor-ggspavis

Visualization functions for spatial transcriptomics data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/ggspavis.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-ggspavis/meta.yaml

Visualization functions for spatial transcriptomics data. Includes functions to generate several types of plots, including spot plots, feature (molecule) plots, reduced dimension plots, spot-level quality control (QC) plots, and feature-level QC plots, for datasets from the 10x Genomics Visium and other technological platforms. Datasets are assumed to be in either SpatialExperiment or SingleCellExperiment format.

package bioconductor-ggspavis

(downloads) docker_bioconductor-ggspavis

versions:

1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0

depends bioconductor-spatialexperiment:

>=1.16.0,<1.17.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-ggplot2:

depends r-ggrepel:

depends r-ggside:

depends r-rcolorbrewer:

depends r-scales:

requirements:

additional platforms:

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-ggspavis

and update with::

   mamba update bioconductor-ggspavis

To create a new environment, run:

mamba create --name myenvname bioconductor-ggspavis

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-ggspavis:<tag>

(see `bioconductor-ggspavis/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-ggspavis/README.html)