recipe bioconductor-escher

Unified multi-dimensional visualizations with Gestalt principles

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-escher/meta.yaml

The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to spatially-resolved transcriptomics data, but also broadly to data visualized in 2D space, such as embedding visualizations. We provide this open source R package escheR, which is built off of the state-of-the-art ggplot2 visualization framework and can be seamlessly integrated into genomics toolboxes and workflows.

package bioconductor-escher

versions:

1.2.0-0,  1.0.0-0

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-ggplot2:

depends r-rlang:

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-escher

and update with::

   mamba update bioconductor-escher

To create a new environment, run:

mamba create --name myenvname bioconductor-escher

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-escher:<tag>

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

Download stats

Link to this page

Render an 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-escher/README.html)