recipe bioconductor-cpvsnp

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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/cpvSNP.html

License

Artistic-2.0

Recipe

/bioconductor-cpvsnp/meta.yaml

Links

biotools: cpvsnp, doi: 10.1038/nmeth.3252

package bioconductor-cpvsnp

(downloads) docker_bioconductor-cpvsnp

Versions

1.16.0-1, 1.14.0-0, 1.12.0-0, 1.10.0-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-cpvsnp

and update with:

conda update bioconductor-cpvsnp

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-cpvsnp:<tag>

(see bioconductor-cpvsnp/tags for valid values for <tag>)