recipe bioconductor-tidycoverage

Extract and aggregate genomic coverage over features of interest

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/tidyCoverage.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-tidycoverage/meta.yaml

`tidyCoverage` framework enables tidy manipulation of collections of genomic tracks and features using `tidySummarizedExperiment` methods. It facilitates the extraction, aggregation and visualization of genomic coverage over individual or thousands of genomic loci, relying on `CoverageExperiment` and `AggregatedCoverage` classes. This accelerates the integration of genomic track data in genomic analysis workflows.

package bioconductor-tidycoverage

versions:

1.2.0-0

depends bioconductor-biocio:

>=1.16.0,<1.17.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-rtracklayer:

>=1.66.0,<1.67.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-cli:

depends r-dplyr:

depends r-fansi:

depends r-ggplot2:

depends r-pillar:

depends r-purrr:

depends r-rlang:

depends r-scales:

depends r-tidyr:

depends r-vctrs:

requirements:

additional platforms:

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-tidycoverage

and update with::

   mamba update bioconductor-tidycoverage

To create a new environment, run:

mamba create --name myenvname bioconductor-tidycoverage

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-tidycoverage:<tag>

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

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