recipe bioconductor-multiassayexperiment

Software for the integration of multi-omics experiments in Bioconductor

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-multiassayexperiment/meta.yaml

Links:

biotools: multiassayexperiment, doi: 10.1101/144774

MultiAssayExperiment harmonizes data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.

package bioconductor-multiassayexperiment

versions:

1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0, 

1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.4-0,  1.8.1-0,  1.6.0-0,  1.4.9-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocbaseutils:

>=1.4.0,<1.5.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-tidyr:

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-multiassayexperiment

and update with::

   mamba update bioconductor-multiassayexperiment

To create a new environment, run:

mamba create --name myenvname bioconductor-multiassayexperiment

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-multiassayexperiment:<tag>

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

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