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Number of citations per year for the bioinformatics software tool GARFIELD
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GARFIELD specifications

Information


Unique identifier OMICS_14270
Name GARFIELD
Alternative name GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data Genomic positions of pruned variants, p-values for association with the trait of interest, number of LD tags (r2>0.8), MAF, distance to the nearest TSS and binary representation of annotation information, enrichment analysis results for each annotation
Output format FILE.PREP, FILE.PERM
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.9.1
Stability Stable
Requirements
knitr
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Nicole Soranzo

Publication for GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

GARFIELD citations

 (3)
library_books

Effects of Type 1 Diabetes Risk Alleles on Immune Cell Gene Expression

2017
Genes
PMCID: 5485531
PMID: 28635624
DOI: 10.3390/genes8060167

[…] ysis can be separately applied to up- and down-regulated genes so as to identify functions that are either magnified or diminished in relation to susceptibility.Other popular enrichment tools such as GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction (GARFIELD) [] and Genomic Regulatory Elements and Gwas Overlap algorithm (GREGOR) [] also provide cross-verification […]

library_books

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

2016
Cell
PMCID: 5119954
PMID: 27863251
DOI: 10.1016/j.cell.2016.10.026

[…] e QTLs based on our WGS data using plink () and 500 kb window.In order to systematically measure the statistical significance of the overlaps between GWAS disease variants and molecular QTLs, we used GARFIELD (), a novel enrichment analysis approach taking genome-wide association summary statistics to calculate odds ratios for association between annotation overlap and disease status at given GWAS […]

library_books

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

2016
Cell
PMCID: 5300907
PMID: 27863252
DOI: 10.1016/j.cell.2016.10.042

[…] our genomic control adjustments.In order to measure systematically the statistical significance of the overlaps between our blood cell index-associated variants and BLUEPRINT epigenetic data, we used GARFIELD (), a novel enrichment analysis approach that uses genome-wide association summary statistics to calculate odds ratios for association between annotation overlap and disease status at given g […]


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GARFIELD institution(s)
Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK; MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Department of Haematology, University of Cambridge, Cambridge, UK; The National Institute for Health Research Blood and Transplant Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
GARFIELD funding source(s)
Wellcome Trust under awards WT098051 and WT091310; MRC Integrative Epidemiology Unit (Medical Research Council MC_UU_12013/3); EMBL-WTSI

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