:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-exomecopy' .. highlight: bash bioconductor-exomecopy ====================== .. conda:recipe:: bioconductor-exomecopy :replaces_section_title: :noindex: Copy number variant detection from exome sequencing read depth :homepage: https://bioconductor.org/packages/3.18/bioc/html/exomeCopy.html :license: GPL (>= 2) :recipe: /`bioconductor-exomecopy `_/`meta.yaml `_ :links: biotools: :biotools:`exomecopy`, doi: :doi:`10.2202/1544-6115.1732` Detection of copy number variants \(CNV\) from exome sequencing samples\, including unpaired samples. The package implements a hidden Markov model which uses positional covariates\, such as background read depth and GC\-content\, to simultaneously normalize and segment the samples into regions of constant copy count. .. conda:package:: bioconductor-exomecopy |downloads_bioconductor-exomecopy| |docker_bioconductor-exomecopy| :versions: .. raw:: html
1.48.0-01.46.0-01.44.0-11.44.0-01.40.0-21.40.0-11.40.0-01.38.0-01.36.0-1 ``1.48.0-0``,  ``1.46.0-0``,  ``1.44.0-1``,  ``1.44.0-0``,  ``1.40.0-2``,  ``1.40.0-1``,  ``1.40.0-0``,  ``1.38.0-0``,  ``1.36.0-1``,  ``1.36.0-0``,  ``1.34.0-0``,  ``1.32.0-0``,  ``1.30.0-1``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-0`` .. raw:: html
:depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomeinfodb: ``>=1.38.1,<1.39.0a0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicranges: ``>=1.54.1,<1.55.0a0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends r-base: ``>=4.3,<4.4.0a0`` :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-exomecopy and update with:: mamba update bioconductor-exomecopy To create a new environment, run:: mamba create --name myenvname bioconductor-exomecopy 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-exomecopy: (see `bioconductor-exomecopy/tags`_ for valid values for ````) .. |downloads_bioconductor-exomecopy| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-exomecopy.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-exomecopy :alt: (downloads) .. |docker_bioconductor-exomecopy| image:: https://quay.io/repository/biocontainers/bioconductor-exomecopy/status :target: https://quay.io/repository/biocontainers/bioconductor-exomecopy .. _`bioconductor-exomecopy/tags`: https://quay.io/repository/biocontainers/bioconductor-exomecopy?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-exomecopy/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-exomecopy/README.html