- 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:
- 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
- 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¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-cpvsnp/README.html)