recipe bioconductor-qdnaseq

Quantitative DNA Sequencing for Chromosomal Aberrations







biotools: qdnaseq

Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

package bioconductor-qdnaseq

(downloads) docker_bioconductor-qdnaseq



depends bioconductor-biobase:


depends bioconductor-cghbase:


depends bioconductor-cghcall:


depends bioconductor-dnacopy:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-rsamtools:


depends r-base:


depends r-future.apply:


depends r-matrixstats:


depends r-r.utils:




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-qdnaseq

and update with::

   mamba update bioconductor-qdnaseq

To create a new environment, run:

mamba create --name myenvname bioconductor-qdnaseq

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-qdnaseq/tags`_ for valid values for ``<tag>``)

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