recipe bioconductor-ogre

Calculate, visualize and analyse overlap between genomic regions

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-ogre/meta.yaml

OGRE calculates overlap between user defined genomic region datasets. Any regions can be supplied i.e. genes, SNPs, or reads from sequencing experiments. Key numbers help analyse the extend of overlaps which can also be visualized at a genomic level.

package bioconductor-ogre

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-gviz:

>=1.46.0,<1.47.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-assertthat:

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dt:

depends r-ggplot2:

depends r-shiny:

depends r-shinybs:

depends r-shinydashboard:

depends r-shinyfiles:

depends r-tidyr:

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-ogre

and update with::

   mamba update bioconductor-ogre

To create a new environment, run:

mamba create --name myenvname bioconductor-ogre

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-ogre:<tag>

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

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