recipe bioconductor-mdts

Detection of de novo deletion in targeted sequencing trios

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/MDTS.html

License:

Artistic-2.0

Recipe:

/bioconductor-mdts/meta.yaml

A package for the detection of de novo copy number deletions in targeted sequencing of trios with high sensitivity and positive predictive value.

package bioconductor-mdts

versions:

1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1, 

1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-dnacopy:

>=1.74.0,<1.75.0

depends bioconductor-genomicalignments:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-rsamtools:

>=2.16.0,<2.17.0

depends r-base:

>=4.3,<4.4.0a0

depends r-stringr:

requirements:

Installation

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-mdts

and update with::

   mamba update bioconductor-mdts

To create a new environment, run:

mamba create --name myenvname bioconductor-mdts

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-mdts:<tag>

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

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