:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-metagene2' .. highlight: bash bioconductor-metagene2 ====================== .. conda:recipe:: bioconductor-metagene2 :replaces_section_title: :noindex: A package to produce metagene plots :homepage: https://bioconductor.org/packages/3.18/bioc/html/metagene2.html :license: Artistic-2.0 :recipe: /`bioconductor-metagene2 `_/`meta.yaml `_ This package produces metagene plots to compare coverages of sequencing experiments at selected groups of genomic regions. It can be used for such analyses as assessing the binding of DNA\-interacting proteins at promoter regions or surveying antisense transcription over the length of a gene. The metagene2 package can manage all aspects of the analysis\, from normalization of coverages to plot facetting according to experimental metadata. Bootstraping analysis is used to provide confidence intervals of per\-sample mean coverages. .. conda:package:: bioconductor-metagene2 |downloads_bioconductor-metagene2| |docker_bioconductor-metagene2| :versions: ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-1`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-data.table: :depends r-dplyr: :depends r-ggplot2: :depends r-magrittr: :depends r-purrr: :depends r-r6: ``>=2.0`` :depends r-reshape2: :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-metagene2 and update with:: mamba update bioconductor-metagene2 To create a new environment, run:: mamba create --name myenvname bioconductor-metagene2 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-metagene2: (see `bioconductor-metagene2/tags`_ for valid values for ````) .. |downloads_bioconductor-metagene2| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-metagene2.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-metagene2 :alt: (downloads) .. |docker_bioconductor-metagene2| image:: https://quay.io/repository/biocontainers/bioconductor-metagene2/status :target: https://quay.io/repository/biocontainers/bioconductor-metagene2 .. _`bioconductor-metagene2/tags`: https://quay.io/repository/biocontainers/bioconductor-metagene2?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-metagene2/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-metagene2/README.html