recipe bioconductor-trio

Testing of SNPs and SNP Interactions in Case-Parent Trio Studies

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/trio.html

License:

LGPL-2

Recipe:

/bioconductor-trio/meta.yaml

Links:

biotools: trio, doi: 10.1038/nmeth.3252

Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.

package bioconductor-trio

(downloads) docker_bioconductor-trio

versions:
3.44.0-0,  3.40.0-0,  3.38.0-0,  3.36.0-0,  3.32.0-0,  3.30.0-0,  3.28.0-1,  3.28.0-0,  3.26.0-0, 

3.44.0-0,  3.40.0-0,  3.38.0-0,  3.36.0-0,  3.32.0-0,  3.30.0-0,  3.28.0-1,  3.28.0-0,  3.26.0-0,  3.24.0-0,  3.22.0-1,  3.20.0-0,  3.18.0-0,  3.16.0-0,  3.14.0-0

depends bioconductor-siggenes:

>=1.80.0,<1.81.0

depends r-base:

>=4.4,<4.5.0a0

depends r-logicreg:

>=1.6.1

depends r-survival:

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-trio

and update with::

   mamba update bioconductor-trio

To create a new environment, run:

mamba create --name myenvname bioconductor-trio

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-trio:<tag>

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

Download stats

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-trio/README.html)