garfield
This is the development version of garfield; for the stable release version, see garfield.
All Bioconductor versions of garfield
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
GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
Bioconductor version: 3.24 · Package version: 1.41.0
GARFIELD is a non-parametric functional enrichment analysis approach described in the paper GARFIELD: GWAS analysis of regulatory or functional information enrichment with LD correction. Briefly, it is a method that leverages GWAS findings with regulatory or functional annotations (primarily from ENCODE and Roadmap epigenomics data) to find features relevant to a phenotype of interest. It performs greedy pruning of GWAS SNPs (LD r2 > 0.1) and then annotates them based on functional information overlap. Next, it quantifies Fold Enrichment (FE) at various GWAS significance cutoffs and assesses them by permutation testing, while matching for minor allele frequency, distance to nearest transcription start site and number of LD proxies (r2 > 0.8).
Author: Sandro Morganella <sm22 at sanger.ac.uk>
Maintainer: Valentina Iotchkova <vi1 at sanger.ac.uk>
Citation
From within R, enter citation("garfield"):
Sandro Morganella. garfield: GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction. doi:10.18129/B9.bioc.garfield, R package version 1.41.0, https://bioconductor.org/packages/garfield.
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("garfield")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.41.0 |
| License | GPL-3 |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10 years) |
| Downloads rank | 2096 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, FunctionalPrediction, GenomeAnnotation, Software, StatisticalMethod |
| Package Short Url | https://bioconductor.org/packages/garfield/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("garfield")| garfield Guide | |
| Reference Manual | |
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | garfield_1.41.0.tar.gz |
| Windows binary (x86_64) | garfield_1.41.0.zip |
| macOS binary (arm64) | garfield_1.41.0.tgz |
| macOS binary (x86_64) | garfield_1.41.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/garfield |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/garfield |
| Package Downloads Report | Download Stats |
Dependencies
Suggests: knitr