recipe bioconductor-biovizbase

Basic graphic utilities for visualization of genomic data.

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-biovizbase/meta.yaml

Links:

biotools: biovizbase, doi: 10.1038/nmeth.3252

The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.

package bioconductor-biovizbase

versions:

1.48.0-0,  1.46.0-1,  1.46.0-0,  1.42.0-2,  1.42.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-1,  1.38.0-0, 

1.48.0-0,  1.46.0-1,  1.46.0-0,  1.42.0-2,  1.42.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-1,  1.38.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-1,  1.30.1-0,  1.30.0-0,  1.28.2-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-annotationfilter:

>=1.24.0,<1.25.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-ensembldb:

>=2.24.0,<2.25.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicalignments:

>=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-iranges:

>=2.34.0,<2.35.0

depends bioconductor-rsamtools:

>=2.16.0,<2.17.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends bioconductor-variantannotation:

>=1.46.0,<1.47.0

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

depends r-dichromat:

depends r-hmisc:

depends r-rcolorbrewer:

depends r-rlang:

depends r-scales:

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-biovizbase

and update with::

   mamba update bioconductor-biovizbase

To create a new environment, run:

mamba create --name myenvname bioconductor-biovizbase

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-biovizbase:<tag>

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

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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-biovizbase/README.html)