recipe r-locuszoomr

Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots.

Homepage:

https://github.com/myles-lewis/locuszoomr

License:

GPL3 / GPL-3

Recipe:

/r-locuszoomr/meta.yaml

package r-locuszoomr

(downloads) docker_r-locuszoomr

versions:

0.3.5-0

depends bioconductor-annotationfilter:

depends bioconductor-biocgenerics:

depends bioconductor-ensembldb:

depends bioconductor-genomeinfodb:

depends bioconductor-genomicranges:

depends bioconductor-iranges:

depends bioconductor-rtracklayer:

depends r-base:

>=4.3,<4.4.0a0

depends r-cowplot:

depends r-dplyr:

depends r-gggrid:

depends r-ggplot2:

depends r-ggrepel:

depends r-ldlinkr:

depends r-memoise:

depends r-plotly:

depends r-rlang:

depends r-zoo:

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 r-locuszoomr

and update with::

   mamba update r-locuszoomr

To create a new environment, run:

mamba create --name myenvname r-locuszoomr

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/r-locuszoomr:<tag>

(see `r-locuszoomr/tags`_ for valid values for ``<tag>``)

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Link to this page

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