:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-cindex' .. highlight: bash bioconductor-cindex =================== .. conda:recipe:: bioconductor-cindex :replaces_section_title: :noindex: Chromosome Instability Index :homepage: https://bioconductor.org/packages/3.18/bioc/html/CINdex.html :license: GPL (>= 2) :recipe: /`bioconductor-cindex `_/`meta.yaml `_ :links: biotools: :biotools:`cindex`, doi: :doi:`10.1038/nmeth.3252` The CINdex package addresses important area of high\-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability \(CIN\) index that allows to quantitatively characterize genome\-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability\, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level. .. conda:package:: bioconductor-cindex |downloads_bioconductor-cindex| |docker_bioconductor-cindex| :versions: .. raw:: html
1.30.0-01.28.0-01.26.0-01.22.0-01.20.0-01.18.0-11.18.0-01.16.0-01.14.0-0 ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-0``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-1``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.10.0-1``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0`` .. raw:: html
: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-s4vectors: ``>=0.40.0,<0.41.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-bitops: :depends r-dplyr: :depends r-gplots: :depends r-gridextra: :depends r-png: :depends r-som: :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-cindex and update with:: mamba update bioconductor-cindex To create a new environment, run:: mamba create --name myenvname bioconductor-cindex 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-cindex: (see `bioconductor-cindex/tags`_ for valid values for ````) .. |downloads_bioconductor-cindex| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-cindex.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-cindex :alt: (downloads) .. |docker_bioconductor-cindex| image:: https://quay.io/repository/biocontainers/bioconductor-cindex/status :target: https://quay.io/repository/biocontainers/bioconductor-cindex .. _`bioconductor-cindex/tags`: https://quay.io/repository/biocontainers/bioconductor-cindex?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-cindex/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-cindex/README.html