recipe bioconductor-massarray

Analytical Tools for MassArray Data

Homepage:

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

License:

GPL (>=2)

Recipe:

/bioconductor-massarray/meta.yaml

Links:

biotools: massarray, doi: 10.1093/bioinformatics/btp382

This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis.

package bioconductor-massarray

(downloads) docker_bioconductor-massarray

versions:
1.54.0-1,  1.54.0-0,  1.52.0-0,  1.50.0-0,  1.46.0-0,  1.44.0-0,  1.42.0-1,  1.42.0-0,  1.40.0-0, 

1.54.0-1,  1.54.0-0,  1.52.0-0,  1.50.0-0,  1.46.0-0,  1.44.0-0,  1.42.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.36.0-0,  1.34.1-0,  1.32.0-0,  1.30.0-0,  1.28.0-0

depends r-base:

>=4.3,<4.4.0a0

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-massarray

and update with::

   mamba update bioconductor-massarray

To create a new environment, run:

mamba create --name myenvname bioconductor-massarray

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-massarray:<tag>

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

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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-massarray/README.html)