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Protocols

HelixTree specifications

Information


Unique identifier OMICS_34296
Name HelixTree
Software type Application/Script
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux
License Commercial
Computer skills Medium
Stability Stable
Registration required Yes
Maintained Yes

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HelixTree citations

 (105)
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HIV 1 Subtypes and 5′LTR Leader Sequence Variants Correlate with Seroconversion Status in Pumwani Sex Worker Cohort

2017
Viruses
PMCID: 5795417
PMID: 29295533
DOI: 10.3390/v10010004
call_split See protocol

[…] applied successfully in genetics, clinical medicine, and bioinformatics within the past few years []. In this study, we used the recursive partitioning methods based interactive tree analysis tool in HelixTree SNP and Variation Suite version 6.4.3 (Golden Helix, Inc., Bozeman, MT, USA) to analyze the large pool of sequence variants of the three important sites (PBS, SD, and PS) within the 5′LTR le […]

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Growth Differentiation Factor 15 May Predict Mortality of Peripheral and Coronary Artery Diseases and Correlate with Their Risk Factors

2017
PMCID: 5535745
PMID: 28798540
DOI: 10.1155/2017/9398401
call_split See protocol

[…] uilibrium (HWE) was assessed using Fisher's exact test. Measures of pairwise linkage disequilibrium (LD) and haplotype frequencies were estimated using the expected maximization algorithm (EM) in the HelixTree Genetics Analysis software (Golden Helix). A linear regression in Golden Helix was applied to capture the major effect of each polymorphism on the log-GDF15, with age, sex, BMI, and smoking […]

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Association Between a Polymorphism in CASP3 and CASP9 Genes and Ischemic Stroke

2017
PMCID: 5426270
PMID: 28503451
DOI: 10.5535/arm.2017.41.2.197
call_split See protocol

[…] using an ABI PRISM 3730XL analyzer (Applied Biosystems, Foster City, CA, USA). Sequence data were analyzed using SeqMan II software (DNASTAR Inc., Madison, WI, USA). To analyze genetic data, we used HelixTree (Golden Helix Inc., Bozeman, MT, USA), SNPStats (http://bioinfo.iconcologia.net/SNPstats), and SNPAnalyzer (ISTECH Inc., Goyang, Korea). […]

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Genetic variants in telomere‐maintenance genes are associated with ovarian cancer risk and outcome

2016
J Cell Mol Med
PMCID: 5323825
PMID: 28233473
DOI: 10.1111/jcmm.12995

[…] log‐rank tests were used to compare the OS differences by different genotypes. Higher order gene–gene interactions were explored using the Classification and Regression Tree analysis, performed using HelixTree Software (Golden Helix, Bozeman, MT, USA). Survival tree analysis was performed using the STREE program (http://masal.med.yale.edu/stree/), which also uses recursive partitioning method. Pla […]

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Identification of genetic modifiers of age at onset for familial Parkinson’s disease

2016
Hum Mol Genet
PMCID: 5216611
PMID: 27402877
DOI: 10.1093/hmg/ddw206
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[…] ontrol measures (genotype and phenotype data for NGRC are available on dbGaP; http://www.ncbi.nlm.nih.gov/gap, accession number phs000196.v2.p1). Principal component analysis (PCA) was conducted with HelixTree (http://www.goldenhelix.com) using a pruned subset of 104,064 SNPs, as described previously (). No association was detected between PC 1-4 and age-at-onset in all PD (P-values for PC 1-4 = 0 […]

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Polymorphism of Nitric Oxide Synthase 1 Affects the Clinical Phenotypes of Ischemic Stroke in South Korean Population

2016
PMCID: 4775742
PMID: 26949676
DOI: 10.5535/arm.2016.40.1.102
call_split See protocol

[…] eral factors including mutations, natural selection, nonrandom mating, and genetic drift. A significant result (p<0.05) means that controls are not in HWE []. SNPAnalyzer-Pro (ISTECH, Goyang, Korea), HelixTree (Golden Helix, Bozeman, United States), and SNPStats (http://bioinfo.iconcologia.net/index.php?module=Snpstats) were used to analyze genetic data. Multiple logistic regression models (codomi […]


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HelixTree institution(s)
Thermo Fisher, Waltham, MA, USA

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