recipe bioconductor-cindex

Chromosome Instability Index



GPL (>= 2)




biotools: cindex, 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.

package bioconductor-cindex

(downloads) docker_bioconductor-cindex



depends bioconductor-genomeinfodb:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-s4vectors:


depends r-base:


depends r-bitops:

depends r-dplyr:

depends r-gplots:

depends r-gridextra:

depends r-png:

depends r-som:

depends r-stringr:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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<tag>

(see `bioconductor-cindex/tags`_ for valid values for ``<tag>``)

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