GUESSFM specifications

Information


Unique identifier OMICS_11300
Name GUESSFM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.0.1
Stability Stable
Requirements
ggplot2, snpStats, VGAM, ggbio, libgsl, guessfm
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Chris Wallace <>

Publication for GUESSFM

GUESSFM in publications

 (2)
PMCID: 5719131
PMID: 28983737
DOI: 10.1007/s00125-017-4440-y

[…] in aad-associated regions (p < 5 × 10−8), we imputed snps to obtain the densest snp set possible in that region, and performed fine-mapping to identify groups of candidate causal snps. we used guessfm (https://github.com/chr1swallace/guessfm version 1.0.1), [] a fine-mapping algorithm [, ] that allows more than one causal snp in the region to be identified. briefly, guessfm identifies […]

PMCID: 5584004
PMID: 28870212
DOI: 10.1186/s13059-017-1285-0

[…] variants in each of the 179 regions where a minimum p < 0.0001 was observed using a stochastic search method which allows for multiple causal variants in a region (https://github.com/chr1swallace/guessfm) []. despite the pre-selection of regions associating with autoimmune diseases on the immunochip, we chose to again set the prior probability that any variant was causal to 10−4, to align […]


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GUESSFM institution(s)
JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK; MRC Biostatistics Unit, Cambridge Institute of Public Health, Cambridge, UK; Centre for Biostatistics Institute of Population Health, The University of Manchester, UK; Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA; Department of Medicine, Division of Endocrinology, University of Virginia, Charlottesville, VA, USA; Department of Public Health Sciences, Division of Biostatistics and Epidemiology, University of Virginia, Charlottesville, VA, USA; University of Cambridge, Department of Clinical Neurosciences, Cambridge, UK
GUESSFM funding source(s)
Supported by the JDRF (9-2011-253), the Wellcome Trust [091157] and the National Institute for Health Research Cambridge Biomedical Centre.

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