:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-metagene' .. highlight: bash bioconductor-metagene ===================== .. conda:recipe:: bioconductor-metagene :replaces_section_title: :noindex: A package to produce metagene plots :homepage: https://bioconductor.org/packages/3.17/bioc/html/metagene.html :license: Artistic-2.0 | file LICENSE :recipe: /`bioconductor-metagene `_/`meta.yaml `_ This package produces metagene plots to compare the behavior of DNA\-interacting proteins at selected groups of genes\/features. Bam files are used to increase the resolution. Multiple combination of group of bam files and\/or group of genomic regions can be compared in a single analysis. Bootstraping analysis is used to compare the groups and locate regions with statistically different enrichment profiles. .. conda:package:: bioconductor-metagene |downloads_bioconductor-metagene| |docker_bioconductor-metagene| :versions: ``2.31.0-0``,  ``2.30.0-0``,  ``2.26.0-0``,  ``2.24.0-0``,  ``2.20.0-0``,  ``2.18.0-0``,  ``2.16.0-1``,  ``2.14.0-0`` :depends bioconductor-biocparallel: ``>=1.34.0,<1.35.0`` :depends bioconductor-ensdb.hsapiens.v86: ``>=2.99.0,<2.100.0`` :depends bioconductor-ensembldb: ``>=2.24.0,<2.25.0`` :depends bioconductor-genomeinfodb: ``>=1.36.0,<1.37.0`` :depends bioconductor-genomicalignments: ``>=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-iranges: ``>=2.34.0,<2.35.0`` :depends bioconductor-rsamtools: ``>=2.16.0,<2.17.0`` :depends bioconductor-rtracklayer: ``>=1.60.0,<1.61.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-data.table: :depends r-ggplot2: :depends r-gplots: :depends r-magrittr: :depends r-matrixstats: :depends r-purrr: :depends r-r6: ``>=2.0`` :depends r-stringr: :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-metagene and update with:: mamba update bioconductor-metagene To create a new environment, run:: mamba create --name myenvname bioconductor-metagene 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-metagene: (see `bioconductor-metagene/tags`_ for valid values for ````) .. |downloads_bioconductor-metagene| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-metagene.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-metagene :alt: (downloads) .. |docker_bioconductor-metagene| image:: https://quay.io/repository/biocontainers/bioconductor-metagene/status :target: https://quay.io/repository/biocontainers/bioconductor-metagene .. _`bioconductor-metagene/tags`: https://quay.io/repository/biocontainers/bioconductor-metagene?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-metagene/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-metagene/README.html