recipe bioconductor-cpvsnp

Gene set analysis methods for SNP association p-values that lie in genes in given gene sets

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-cpvsnp/meta.yaml

Links:

biotools: cpvsnp, doi: 10.1038/nmeth.3252

Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results.

package bioconductor-cpvsnp

(downloads) docker_bioconductor-cpvsnp

Versions:
1.42.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0, 

1.42.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0

Depends:

  • on bioconductor-biocparallel >=1.44.0,<1.45.0

  • on bioconductor-genomicfeatures >=1.62.0,<1.63.0

  • on bioconductor-gseabase >=1.72.0,<1.73.0

  • on r-base >=4.5,<4.6.0a0

  • on r-corpcor

  • on r-ggplot2

  • on r-plyr

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-cpvsnp

to add into an existing workspace instead, run:

pixi add bioconductor-cpvsnp

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-cpvsnp

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-cpvsnp

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-cpvsnp:<tag>

(see bioconductor-cpvsnp/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.

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