recipe bioconductor-raggedexperiment

Representation of Sparse Experiments and Assays Across Samples

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/RaggedExperiment.html

License:

Artistic-2.0

Recipe:

/bioconductor-raggedexperiment/meta.yaml

This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns. The RaggedExperiment class derives from a GRangesList representation and provides a semblance of a rectangular dataset.

package bioconductor-raggedexperiment

versions:

1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.1-0,  1.14.0-0,  1.12.0-0, 

1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.1-0,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-biocbaseutils:

>=1.8.0,<1.9.0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-matrixgenerics:

>=1.18.0,<1.19.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-matrix:

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-raggedexperiment

and update with::

   mamba update bioconductor-raggedexperiment

To create a new environment, run:

mamba create --name myenvname bioconductor-raggedexperiment

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-raggedexperiment:<tag>

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

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