recipe bioconductor-geomxtools

NanoString GeoMx Tools

Homepage:

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

License:

MIT

Recipe:

/bioconductor-geomxtools/meta.yaml

Tools for NanoString Technologies GeoMx Technology. Package provides functions for reading in DCC and PKC files based on an ExpressionSet derived object. Normalization and QC functions are also included.

package bioconductor-geomxtools

versions:

3.10.0-0,  3.5.0-0,  3.4.0-0,  3.2.0-0,  2.0.0-0,  1.0.0-0

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-nanostringnctools:

>=1.14.0,<1.15.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends r-base:

>=4.4,<4.5.0a0

depends r-data.table:

depends r-dplyr:

depends r-envstats:

depends r-ggally:

depends r-ggplot2:

depends r-lmertest:

depends r-readxl:

depends r-reshape2:

depends r-rjson:

depends r-rlang:

depends r-seuratobject:

depends r-stringr:

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-geomxtools

and update with::

   mamba update bioconductor-geomxtools

To create a new environment, run:

mamba create --name myenvname bioconductor-geomxtools

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-geomxtools:<tag>

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

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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-geomxtools/README.html)