recipe bioconductor-genomicdistributions

GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Homepage:

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

License:

BSD_2_clause + file LICENSE

Recipe:

/bioconductor-genomicdistributions/meta.yaml

If you have a set of genomic ranges, this package can help you with visualization and comparison. It produces several kinds of plots, for example: Chromosome distribution plots, which visualize how your regions are distributed over chromosomes; feature distance distribution plots, which visualizes how your regions are distributed relative to a feature of interest, like Transcription Start Sites (TSSs); genomic partition plots, which visualize how your regions overlap given genomic features such as promoters, introns, exons, or intergenic regions. It also makes it easy to compare one set of ranges to another.

package bioconductor-genomicdistributions

versions:

1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends r-base:

>=4.3,<4.4.0a0

depends r-broom:

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-plyr:

depends r-reshape2:

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-genomicdistributions

and update with::

   mamba update bioconductor-genomicdistributions

To create a new environment, run:

mamba create --name myenvname bioconductor-genomicdistributions

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-genomicdistributions:<tag>

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

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