:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-coseq' .. highlight: bash bioconductor-coseq ================== .. conda:recipe:: bioconductor-coseq :replaces_section_title: :noindex: Co\-Expression Analysis of Sequencing Data :homepage: https://bioconductor.org/packages/3.18/bioc/html/coseq.html :license: GPL-3 :recipe: /`bioconductor-coseq `_/`meta.yaml `_ Co\-expression analysis for expression profiles arising from high\-throughput sequencing data. Feature \(e.g.\, gene\) profiles are clustered using adapted transformations and mixture models or a K\-means algorithm\, and model selection criteria \(to choose an appropriate number of clusters\) are provided. .. conda:package:: bioconductor-coseq |downloads_bioconductor-coseq| |docker_bioconductor-coseq| :versions: ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-0``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-1``,  ``1.6.0-0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-deseq2: ``>=1.42.0,<1.43.0`` :depends bioconductor-edger: ``>=4.0.0,<4.1.0`` :depends bioconductor-htsfilter: ``>=1.42.0,<1.43.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-capushe: :depends r-compositions: :depends r-corrplot: :depends r-e1071: :depends r-ggplot2: :depends r-htscluster: :depends r-mvtnorm: :depends r-rmixmod: :depends r-scales: :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-coseq and update with:: mamba update bioconductor-coseq To create a new environment, run:: mamba create --name myenvname bioconductor-coseq 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-coseq: (see `bioconductor-coseq/tags`_ for valid values for ````) .. |downloads_bioconductor-coseq| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-coseq.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-coseq :alt: (downloads) .. |docker_bioconductor-coseq| image:: https://quay.io/repository/biocontainers/bioconductor-coseq/status :target: https://quay.io/repository/biocontainers/bioconductor-coseq .. _`bioconductor-coseq/tags`: https://quay.io/repository/biocontainers/bioconductor-coseq?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-coseq/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-coseq/README.html