cpvSNP
This is the development version of cpvSNP; for the stable release version, see cpvSNP.
All Bioconductor versions of cpvSNP
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Bioconductor version: 3.24 · Package version: 1.45.0
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.
Author: Caitlin McHugh, Jessica Larson, and Jason Hackney
Maintainer: Caitlin McHugh <mchughc at uw.edu>
Citation
From within R, enter citation("cpvSNP"):
Caitlin McHugh, Jessica Larson, and Jason Hackney. cpvSNP: Gene set analysis methods for SNP association p-values that lie in genes in given gene sets. doi:10.18129/B9.bioc.cpvSNP, R package version 1.45.0, https://bioconductor.org/packages/cpvSNP.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("cpvSNP")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.45.0 |
| License | Artistic-2.0 |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11 years) |
| Downloads rank | 808 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneSetEnrichment, Genetics, GenomicVariation, Pathways, Software, StatisticalMethod |
| Package Short Url | https://bioconductor.org/packages/cpvSNP/ |
Documentation
| Reference Manual | |
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | cpvSNP_1.45.0.tar.gz |
| Windows binary (x86_64) | cpvSNP_1.45.0.zip |
| macOS binary (arm64) | cpvSNP_1.45.0.tgz |
| macOS binary (x86_64) | cpvSNP_1.45.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cpvSNP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cpvSNP |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 3.5.0), GenomicFeatures, GSEABase (>= 1.24.0)
Imports: methods, corpcor, BiocParallel, ggplot2, plyr
Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle