garfield¶

Description¶

Software GARFIELD (GWAS analysis of regulatory and functional information enrichment with LD correction) implements a functional enrichment analysis approach described in [Iotchkova et al, 2016] using C++ for data pre-processing, and R for enrichment estimation and significance testing and visualisation. GARFIELD leverages GWAS findings with regulatory or functional annotations (primarily from ENCODE and Roadmap epigenomics data) to find features relevant to a phenotype of interest.

Environment Modules¶

Run module spider garfield to find out what environment modules are available for this application.

Environment Variables¶

HPC_GARFIELD_DIR - installation directory
HPC_GARFIELD_BIN - executable directory
HPC_GARFIELD_REF - reference database

Citation¶

If you publish research that uses garfield you have to cite it as follows:

Valentina Iotchkova, Graham R.S. Ritchie, Matthias Geihs, Sandro Morganella, Josine L. Min, Klaudia Walter, Nicholas J. Timpson, UK10K Consortium, Ian Dunham, Ewan Birney and Nicole Soranzo. GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction. doi: https://doi.org/10.1101/085738

Categories¶

genomics