recipe bioconductor-synextend

Tools for Working With Synteny Objects

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-synextend/meta.yaml

Shared order between genomic sequences provide a great deal of information. Synteny objects produced by the R package DECIPHER provides quantitative information about that shared order. SynExtend provides tools for extracting information from Synteny objects.

package bioconductor-synextend

versions:

1.14.0-0,  1.12.0-0,  1.10.2-1,  1.10.2-0,  1.6.0-0,  1.4.1-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-biostrings:

>=2.70.1,<2.71.0a0

depends bioconductor-decipher:

>=2.30.0,<2.31.0

depends bioconductor-decipher:

>=2.30.0,<2.31.0a0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0a0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-s4vectors:

>=0.40.2,<0.41.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

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-synextend

and update with::

   mamba update bioconductor-synextend

To create a new environment, run:

mamba create --name myenvname bioconductor-synextend

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-synextend:<tag>

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

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Link to this page

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-synextend/README.html)