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Synthesis-View specifications

Information


Unique identifier OMICS_11753
Name Synthesis-View
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input format text
Output data Images
Output format PNG, JPG, PDF
Programming languages Ruby
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Scott Dudek <>

Information


Unique identifier OMICS_11753
Name Synthesis-View
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format text
Output data Images
Output format PNG, JPG, PDF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Ruby
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
RMagick
Maintained Yes

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Documentation


Maintainer


  • person_outline Scott Dudek <>

Publication for Synthesis-View

Synthesis-View in publications

 (9)
PMCID: 4989894
PMID: 27535653
DOI: 10.1186/s12920-016-0191-8

[…] logistic regression between 25 snps and 2,859 icd-9 based case/control status and in the replication dataset 2,854 icd-9 codes were included. results of tests of association were visualized using synthesis-view []. because some of the snps might have shown association in one racial/ancestry group compared to another, and one of our proof-of-concept snps is more prevalent in people of african […]

PMCID: 4980020
PMID: 27508393
DOI: 10.1371/journal.pone.0160573

[…] variation. lists the icd-9 categories and descriptions selected through this process, as well as the genes in which the variants are located. this process resulted in 409 associations ()., we used synthesis-view [], phenogram [], and cytoscape [], to visualize the results. synthesis-view was used to visualize the snp-phenotype associations and to plot associations matching previously reported […]

PMCID: 4396430
PMID: 25884002
DOI: 10.1093/ofid/ofu113

[…] for each dataset, as well as the nearest gene(s), and any known gwas catalog associations, at http://ritchielab.psu.edu/publications/supplementary-data/actg-phewas (supplementary table 1)., synthesis-view [] was used to visualize results that replicated gwas catalog associations. phenogram [] was used to visualize results for potentially pleiotropic snps. ggplot2 [] was used to generate […]

PMCID: 4249871
PMID: 25436638
DOI: 10.1371/journal.pone.0111301

[…] quality control and data analysis were performed using a combination of plink ,, and r software, and data were plotted using r code obtained from the getting genetics done website ,, stata and synthesis-view . power calculations were performed using quanto . linear regression was performed assuming an additive genetic model to test for associations between individual snps […]

PMCID: 4185105
PMID: 25085266
DOI: 10.1007/s00439-014-1472-y

[…] and european ancestry. mean waa in aas was 0.79, which was similar to previous estimates in the study populations (batai et al. ). ld patterns were examined using haploview (barrett et al. ). synthesis-view was used to visualize the results of snp associations in linear regression models (pendergrass et al. )., vitamin d deficiency and insufficiency were more common in aas than in eas […]


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Synthesis-View institution(s)
Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Molecular Physiology & Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA
Synthesis-View funding source(s)
This work was funded in part by the following grants: LM010040 and HG004798.

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