- 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/3.18/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:
1.34.0-0
,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
,1.34.0-0
,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 bioconductor-biocparallel:
>=1.36.0,<1.37.0
- depends bioconductor-genomicfeatures:
>=1.54.0,<1.55.0
- depends bioconductor-gseabase:
>=1.64.0,<1.65.0
- depends r-base:
>=4.3,<4.4.0a0
- depends r-corpcor:
- depends r-ggplot2:
- depends r-plyr:
- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-cpvsnp and update with:: mamba update bioconductor-cpvsnp
To create a new environment, run:
mamba create --name myenvname bioconductor-cpvsnp
with
myenvname
being a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, 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:
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-cpvsnp/README.html)