recipe bioconductor-genomeinfodb

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-genomeinfodb/meta.yaml

Links:

biotools: genomeinfodb, doi: 10.1038/nmeth.3252

Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

package bioconductor-genomeinfodb

(downloads) docker_bioconductor-genomeinfodb

versions:
1.42.0-0,  1.38.1-1,  1.38.1-0,  1.36.1-0,  1.34.9-0,  1.34.8-0,  1.34.1-0,  1.30.1-0,  1.30.0-0, 

1.42.0-0,  1.38.1-1,  1.38.1-0,  1.36.1-0,  1.34.9-0,  1.34.8-0,  1.34.1-0,  1.30.1-0,  1.30.0-0,  1.28.0-0,  1.26.4-0,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.18.1-0,  1.16.0-0,  1.14.0-0,  1.12.3-0,  1.10.3-0,  1.8.7-0,  1.6.3-0,  1.6.1-0,  1.6.0-0,  1.4.3-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-genomeinfodbdata:

>=1.2.0,<1.3.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-ucsc.utils:

>=1.2.0,<1.3.0

depends r-base:

>=4.4,<4.5.0a0

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-genomeinfodb

and update with::

   mamba update bioconductor-genomeinfodb

To create a new environment, run:

mamba create --name myenvname bioconductor-genomeinfodb

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-genomeinfodb:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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