Package Recipe 'bioconductor-genomicranges'

recipe bioconductor-genomicranges

Representation and manipulation of genomic intervals

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/GenomicRanges.html
License:: Artistic-2.0
Recipe:: /bioconductor-genomicranges/meta.yaml
Links:: biotools: genomicranges

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.

package bioconductor-genomicranges¶

Versions:

1.62.1-0, 1.58.0-2, 1.58.0-1, 1.58.0-0, 1.54.1-2, 1.54.1-1, 1.54.1-0, 1.52.0-0, 1.50.0-1,

1.62.1-0, 1.58.0-2, 1.58.0-1, 1.58.0-0, 1.54.1-2, 1.54.1-1, 1.54.1-0, 1.52.0-0, 1.50.0-1, 1.50.0-0, 1.46.1-1, 1.46.1-0, 1.46.0-0, 1.44.0-0, 1.42.0-1, 1.42.0-0, 1.40.0-0, 1.38.0-0, 1.36.0-1, 1.34.0-0, 1.32.7-0, 1.30.3-0, 1.30.0-0, 1.28.6-0, 1.26.4-0, 1.26.1-1, 1.24.3-1, 1.22.4-0, 1.22.3-0, 1.22.2-0, 1.22.1-0, 1.22.0-0, 1.20.8-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0a0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-iranges >=2.44.0,<2.45.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-seqinfo >=1.0.0,<1.1.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0

Additional platforms:

linux-aarch64, osx-arm64

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-genomicranges

to add into an existing workspace instead, run:

pixi add bioconductor-genomicranges

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-genomicranges

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-genomicranges

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-genomicranges:<tag>

(see bioconductor-genomicranges/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-genomicranges/README.html)