recipe bioconductor-spatialomicsoverlay

Spatial Overlay for Omic Data from Nanostring GeoMx Data

Homepage:

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

License:

MIT

Recipe:

/bioconductor-spatialomicsoverlay/meta.yaml

Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression.

package bioconductor-spatialomicsoverlay

versions:

1.2.1-0,  1.0.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-ebimage:

>=4.44.0,<4.45.0

depends bioconductor-geomxtools:

>=3.5.0,<3.6.0

depends bioconductor-rbioformats:

>=1.2.0,<1.3.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-base64enc:

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-ggtext:

depends r-magick:

depends r-pbapply:

depends r-plotrix:

depends r-readxl:

depends r-scattermore:

depends r-stringr:

depends r-xml:

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-spatialomicsoverlay

and update with::

   mamba update bioconductor-spatialomicsoverlay

To create a new environment, run:

mamba create --name myenvname bioconductor-spatialomicsoverlay

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-spatialomicsoverlay:<tag>

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

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Link to this page

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-spatialomicsoverlay/README.html)