recipe bioconductor-karyoploter

Plot customizable linear genomes displaying arbitrary data

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-karyoploter/meta.yaml

karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

package bioconductor-karyoploter

versions:

1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0, 

1.28.0-0,  1.26.0-0,  1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.4-0,  1.8.5-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-bamsignals:

>=1.34.0,<1.35.0

depends bioconductor-biovizbase:

>=1.50.0,<1.51.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-regioner:

>=1.34.0,<1.35.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-variantannotation:

>=1.48.0,<1.49.0

depends r-base:

>=4.3,<4.4.0a0

depends r-bezier:

depends r-digest:

depends r-memoise:

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-karyoploter

and update with::

   mamba update bioconductor-karyoploter

To create a new environment, run:

mamba create --name myenvname bioconductor-karyoploter

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-karyoploter:<tag>

(see `bioconductor-karyoploter/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-karyoploter/README.html)