- recipe bioconductor-river
R package for RIVER (RNA-Informed Variant Effect on Regulation)
- Homepage:
- License:
GPL (>= 2)
- Recipe:
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:
1.34.0-0,1.30.0-0,1.26.0-0,1.24.0-0,1.22.0-0,1.18.0-0,1.16.0-0,1.14.0-1,1.14.0-0,1.34.0-0,1.30.0-0,1.26.0-0,1.24.0-0,1.22.0-0,1.18.0-0,1.16.0-0,1.14.0-1,1.14.0-0,1.12.0-0,1.10.0-0,1.8.0-1,1.6.0-0- Depends:
on bioconductor-biobase
>=2.70.0,<2.71.0on r-base
>=4.5,<4.6.0a0on r-ggplot2
on r-glmnet
on r-proc
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install bioconductor-river
to add into an existing workspace instead, run:
pixi add bioconductor-river
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install bioconductor-river
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-river
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/bioconductor-river:<tag>
(see bioconductor-river/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-river/README.html)
