recipe bioconductor-updhmm

Detecting Uniparental Disomy through NGS trio data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/UPDhmm.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-updhmm/meta.yaml

Uniparental disomy (UPD) is a genetic condition where an individual inherits both copies of a chromosome or part of it from one parent, rather than one copy from each parent. This package contains a HMM for detecting UPDs through HTS (High Throughput Sequencing) data from trio assays. By analyzing the genotypes in the trio, the model infers a hidden state (normal, father isodisomy, mother isodisomy, father heterodisomy and mother heterodisomy).

package bioconductor-updhmm

versions:

requirements:

additional platforms:

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-updhmm

and update with::

   mamba update bioconductor-updhmm

To create a new environment, run:

mamba create --name myenvname bioconductor-updhmm

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-updhmm:<tag>

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

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