recipe bioconductor-rqt

rqt: utilities for gene-level meta-analysis

Homepage:

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

License:

GPL

Recipe:

/bioconductor-rqt/meta.yaml

Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: "Gene-set association tests for next-generation sequencing data" by Lee et al (2016), Bioinformatics, 32(17), i611-i619, <doi:10.1093/bioinformatics/btw429>.

package bioconductor-rqt

versions:

1.28.0-0,  1.26.0-0,  1.24.0-0,  1.19.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0, 

1.28.0-0,  1.26.0-0,  1.24.0-0,  1.19.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.0-0

depends bioconductor-ropls:

>=1.34.0,<1.35.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-car:

depends r-compquadform:

depends r-glmnet:

depends r-matrix:

depends r-metap:

depends r-pls:

depends r-runit:

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-rqt

and update with::

   mamba update bioconductor-rqt

To create a new environment, run:

mamba create --name myenvname bioconductor-rqt

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-rqt:<tag>

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

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