:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-rlseq' .. highlight: bash bioconductor-rlseq ================== .. conda:recipe:: bioconductor-rlseq :replaces_section_title: :noindex: 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\(\)\`. .. conda:package:: bioconductor-rlseq |downloads_bioconductor-rlseq| |docker_bioconductor-rlseq| :versions: ``1.6.0-0``,  ``1.4.1-0``,  ``1.0.0-0`` :depends bioconductor-annotationhub: ``>=3.8.0,<3.9.0`` :depends bioconductor-complexheatmap: ``>=2.16.0,<2.17.0`` :depends bioconductor-genomeinfodb: ``>=1.36.0,<1.37.0`` :depends bioconductor-genomicfeatures: ``>=1.52.0,<1.53.0`` :depends bioconductor-genomicranges: ``>=1.52.0,<1.53.0`` :depends bioconductor-regioner: ``>=1.32.0,<1.33.0`` :depends bioconductor-rlhub: ``>=1.6.0,<1.7.0`` :depends bioconductor-rtracklayer: ``>=1.60.0,<1.61.0`` :depends r-aws.s3: :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-callr: :depends r-caretensemble: :depends r-circlize: :depends r-dplyr: :depends r-ggplot2: :depends r-ggplotify: :depends r-ggprism: :depends r-pheatmap: :depends r-rcolorbrewer: :depends r-valr: :depends r-venndiagram: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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-rlseq and update with:: mamba update bioconductor-rlseq To create a new environment, run:: mamba create --name myenvname bioconductor-rlseq 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-rlseq: (see `bioconductor-rlseq/tags`_ for valid values for ````) .. |downloads_bioconductor-rlseq| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-rlseq.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-rlseq :alt: (downloads) .. |docker_bioconductor-rlseq| image:: https://quay.io/repository/biocontainers/bioconductor-rlseq/status :target: https://quay.io/repository/biocontainers/bioconductor-rlseq .. _`bioconductor-rlseq/tags`: https://quay.io/repository/biocontainers/bioconductor-rlseq?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-rlseq/README.html