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/3.16/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

Versions:

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, 

1.30.0-0,  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:

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-gseabase >=1.60.0,<1.61.0

• r-base >=4.2,<4.3.0a0

• r-corpcor

• r-ggplot2

• r-plyr

Required By:

Installation

With an activated Bioconda channel (see 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>)

Download stats

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