Package Recipe 'bioconductor-tidycoverage'

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:

1.6.0-0, 1.2.0-0

Depends:

on bioconductor-biocio >=1.20.0,<1.21.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-cli
on r-dplyr
on r-fansi
on r-ggplot2
on r-pillar
on r-purrr
on r-rlang
on r-scales
on r-tidyr
on r-vctrs

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-tidycoverage

to add into an existing workspace instead, run:

pixi add bioconductor-tidycoverage

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-tidycoverage

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-tidycoverage

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-tidycoverage:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-tidycoverage/README.html)