recipe bioconductor-nanotube

An Easy Pipeline for NanoString nCounter Data Analysis

Homepage:

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

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-nanotube/meta.yaml

NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data. Analysis functions include differential analysis and gene set analysis methods, as well as postprocessing steps to help understand the results. Additional functions are included to enable interoperability with other Bioconductor NanoString data analysis packages.

package bioconductor-nanotube

(downloads) docker_bioconductor-nanotube

versions:

1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-fgsea:

>=1.28.0,<1.29.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-reshape:

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-nanotube

and update with::

   mamba update bioconductor-nanotube

To create a new environment, run:

mamba create --name myenvname bioconductor-nanotube

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-nanotube:<tag>

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