recipe bioconductor-tumourmethdata

A Collection of DNA Methylation Datasets for Human Tumour Samples and Matching Normal Samples

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/TumourMethData.html

License:

Artistic-2.0

Recipe:

/bioconductor-tumourmethdata/meta.yaml

TumourMethData collects tumour methylation data from a variety of different tumour types (and also matching normal samples where available) and produced with different technologies (e.g. WGBS, RRBS and methylation arrays) and provides them as RangedSummarizedExperiments. This facilitates easy extraction of methylation data for regions of interest across different tumour types and studies.

package bioconductor-tumourmethdata

versions:

1.0.0-0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-experimenthub:

>=2.10.0,<2.11.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-hdf5array:

>=1.30.0,<1.31.0

depends bioconductor-rhdf5:

>=2.46.0,<2.47.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

depends r-r.utils:

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-tumourmethdata

and update with::

   mamba update bioconductor-tumourmethdata

To create a new environment, run:

mamba create --name myenvname bioconductor-tumourmethdata

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-tumourmethdata:<tag>

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

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Link to this page

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