:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-cnvpanelizer' .. highlight: bash bioconductor-cnvpanelizer ========================= .. conda:recipe:: bioconductor-cnvpanelizer :replaces_section_title: :noindex: Reliable CNV detection in targeted sequencing applications :homepage: https://bioconductor.org/packages/3.18/bioc/html/CNVPanelizer.html :license: GPL-3 :recipe: /`bioconductor-cnvpanelizer `_/`meta.yaml `_ :links: biotools: :biotools:`cnvpanelizer`, doi: :doi:`10.1038/nmeth.3252` A method that allows for the use of a collection of non\-matched normal tissue samples. Our approach uses a non\-parametric bootstrap subsampling of the available reference samples to estimate the distribution of read counts from targeted sequencing. As inspired by random forest\, this is combined with a procedure that subsamples the amplicons associated with each of the targeted genes. The obtained information allows us to reliably classify the copy number aberrations on the gene level. .. conda:package:: bioconductor-cnvpanelizer |downloads_bioconductor-cnvpanelizer| |docker_bioconductor-cnvpanelizer| :versions: .. raw:: html
1.34.0-01.32.0-01.30.0-01.26.0-01.24.0-01.22.0-11.22.0-01.20.0-01.18.0-0 ``1.34.0-0``,  ``1.32.0-0``,  ``1.30.0-0``,  ``1.26.0-0``,  ``1.24.0-0``,  ``1.22.0-1``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-0``,  ``1.16.0-1``,  ``1.14.0-0``,  ``1.12.0-0``,  ``1.8.0-0`` .. raw:: html
:depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-exomecopy: ``>=1.48.0,<1.49.0`` :depends bioconductor-genomeinfodb: ``>=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-noiseq: ``>=2.46.0,<2.47.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-foreach: :depends r-ggplot2: :depends r-gplots: :depends r-openxlsx: :depends r-plyr: :depends r-reshape2: :depends r-shiny: :depends r-shinyfiles: :depends r-shinyjs: :depends r-stringr: :depends r-testthat: :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-cnvpanelizer and update with:: mamba update bioconductor-cnvpanelizer To create a new environment, run:: mamba create --name myenvname bioconductor-cnvpanelizer 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-cnvpanelizer: (see `bioconductor-cnvpanelizer/tags`_ for valid values for ````) .. |downloads_bioconductor-cnvpanelizer| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-cnvpanelizer.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-cnvpanelizer :alt: (downloads) .. |docker_bioconductor-cnvpanelizer| image:: https://quay.io/repository/biocontainers/bioconductor-cnvpanelizer/status :target: https://quay.io/repository/biocontainers/bioconductor-cnvpanelizer .. _`bioconductor-cnvpanelizer/tags`: https://quay.io/repository/biocontainers/bioconductor-cnvpanelizer?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-cnvpanelizer/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-cnvpanelizer/README.html