Package Recipe 'bioconductor-rlseq'

recipe bioconductor-rlseq

RLSeq: An analysis package for R-loop mapping data

Homepage:: https://bioconductor.org/packages/3.18/bioc/html/RLSeq.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-rlseq/meta.yaml

RLSeq is a toolkit for analyzing and evaluating R-loop mapping datasets. RLSeq serves two primary purposes: (1) to facilitate the evaluation of dataset quality, and (2) to enable R-loop analysis in the context of publicly-available data sets from RLBase. The package is intended to provide a simple pipeline, called with the `RLSeq()` function, which performs all main analyses. Individual functions are also accessible and provide custom analysis capabilities. Finally an HTML report is generated with `report()`.

package bioconductor-rlseq¶

Versions:

1.6.0-0, 1.4.1-0, 1.0.0-0

Depends:

on bioconductor-annotationhub >=3.8.0,<3.9.0
on bioconductor-complexheatmap >=2.16.0,<2.17.0
on bioconductor-genomeinfodb >=1.36.0,<1.37.0
on bioconductor-genomicfeatures >=1.52.0,<1.53.0
on bioconductor-genomicranges >=1.52.0,<1.53.0
on bioconductor-regioner >=1.32.0,<1.33.0
on bioconductor-rlhub >=1.6.0,<1.7.0
on bioconductor-rtracklayer >=1.60.0,<1.61.0
on r-aws.s3
on r-base >=4.3,<4.4.0a0
on r-callr
on r-caretensemble
on r-circlize
on r-dplyr
on r-ggplot2
on r-ggplotify
on r-ggprism
on r-pheatmap
on r-rcolorbrewer
on r-valr
on r-venndiagram

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-rlseq

to add into an existing workspace instead, run:

pixi add bioconductor-rlseq

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-rlseq

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-rlseq

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-rlseq:<tag>

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