recipe bioconductor-annotationhubdata

Transform public data resources into Bioconductor Data Structures

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/AnnotationHubData.html

License:

Artistic-2.0

Recipe:

/bioconductor-annotationhubdata/meta.yaml

Links:

biotools: annotationhubdata, doi: 10.1038/nmeth.3252

These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.

package bioconductor-annotationhubdata

versions:

1.30.0-0,  1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.1-0,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1, 

1.30.0-0,  1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.1-0,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.12.0-0,  1.10.3-0,  1.8.0-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-annotationforge:

>=1.42.0,<1.43.0

depends bioconductor-annotationhub:

>=3.8.0,<3.9.0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-bioccheck:

>=1.36.0,<1.37.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biocviews:

>=1.68.0,<1.69.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicfeatures:

>=1.52.0,<1.53.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-graph:

>=1.78.0,<1.79.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-organismdbi:

>=1.42.0,<1.43.0

depends bioconductor-rsamtools:

>=2.16.0,<2.17.0

depends bioconductor-rtracklayer:

>=1.60.0,<1.61.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends r-base:

>=4.3,<4.4.0a0

depends r-biocmanager:

depends r-dbi:

depends r-futile.logger:

>=1.3.0

depends r-jsonlite:

depends r-rcurl:

depends r-rsqlite:

depends r-xml:

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-annotationhubdata

and update with::

   mamba update bioconductor-annotationhubdata

To create a new environment, run:

mamba create --name myenvname bioconductor-annotationhubdata

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-annotationhubdata:<tag>

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

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