recipe bioconductor-river

R package for RIVER (RNA-Informed Variant Effect on Regulation)

Homepage:

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

License:

GPL (>= 2)

Recipe:

/bioconductor-river/meta.yaml

An implementation of a probabilistic modeling framework that jointly analyzes personal genome and transcriptome data to estimate the probability that a variant has regulatory impact in that individual. It is based on a generative model that assumes that genomic annotations, such as the location of a variant with respect to regulatory elements, determine the prior probability that variant is a functional regulatory variant, which is an unobserved variable. The functional regulatory variant status then influences whether nearby genes are likely to display outlier levels of gene expression in that person. See the RIVER website for more information, documentation and examples.

package bioconductor-river

versions:

1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0, 

1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.6.0-0

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends r-base:

>=4.4,<4.5.0a0

depends r-ggplot2:

depends r-glmnet:

depends r-proc:

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-river

and update with::

   mamba update bioconductor-river

To create a new environment, run:

mamba create --name myenvname bioconductor-river

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-river:<tag>

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

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Link to this page

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