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Protocols

Haplin specifications

Information


Unique identifier OMICS_21755
Name Haplin
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 6.2.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Hakon Gjessing
  • person_outline Hakon Gjessing

Additional information


http://folk.uib.no/gjessing/genetics/software/haplin/docu/practical_advice/

Publications for Haplin

Haplin citations

 (21)
library_books

A Genome Wide Search for Gene Environment Effects in Isolated Cleft Lip with or without Cleft Palate Triads Points to an Interaction between Maternal Periconceptional Vitamin Use and Variants in ESRRG

2018
Front Genet
PMCID: 5834486
PMID: 29535761
DOI: 10.3389/fgene.2018.00060

[…] . () for more details on the calculation of RRR.Since its inception, Haplin has incorporated haplotype estimation for triads. By using the expectation-maximization (EM) algorithm (Dempster et al., ), Haplin reconstructs haplotypes from the multi-SNP data even though phase is not known from the observed markers alone. The EM-algorithm also enables Haplin to account for missing parental genotypes, t […]

library_books

Analysis of Parent of Origin Effects on the X Chromosome in Asian and European Orofacial Cleft Triads Identifies Associations with DMD, FGF13, EGFL6, and Additional Loci at Xp22.2

2018
Front Genet
PMCID: 5827165
PMID: 29520293
DOI: 10.3389/fgene.2018.00025

[…] ture studies of PoO effects in OFCs. In addition, scenarios involving variable escape from X-chromosome inactivation (Peeters et al., ) are also amenable to testing using the X-inactivation models in Haplin.Identifying associations between isolated OFCs and genes for clefting syndromes is not surprising, as it has long been recognized that Mendelian forms of clefting that phenocopy isolated clefts […]

call_split

Association of ARID5B Genetic Variants with Risk of Childhood B Cell Precursor Acute Lymphoblastic Leukaemia in Latvia

2018
PMCID: 5844642
PMID: 29373897
DOI: 10.22034/APJCP.2018.19.1.91
call_split See protocol

[…] and family study model statistical result gathering, and for increasing the statistical confidence in these results, a hybrid analysis was used, in which analysis was performed, using the R software, Haplin package, which is based on a log-linear model, and if necessary, uses – expectation–maximization algorithm for haplotype reconstruction (Gjessing and Lie, 2006; Hosseini Teshnizi and Taghi Ayat […]

library_books

Parent‐of‐origin‐environment interactions in case‐parent triads with or without independent controls

2017
Ann Hum Genet
PMCID: 5813215
PMID: 29094765
DOI: 10.1111/ahg.12224

[…] Haplin is implemented as a standard package in the statistical software R (R Core Team, ) and can be installed from the official R package archive, CRAN (https://cran.r‐project.org). Our website (http […]

call_split

A new approach to chromosome wide analysis of X linked markers identifies new associations in Asian and European case parent triads of orofacial clefts

2017
PLoS One
PMCID: 5587310
PMID: 28877219
DOI: 10.1371/journal.pone.0183772
call_split See protocol

[…] HAPLIN version 6.0.1 [] was used to analyze one SNP at a time in single-marker analyses, and a maximum of four consecutive SNPs per window in sliding-window haplotype analyses. HAPLIN fits a log-linea […]

library_books

Investigation of previously implicated genetic variants in chronic tic disorders: a transmission disequilibrium test approach

2017
PMCID: 5708161
PMID: 28555406
DOI: 10.1007/s00406-017-0808-8

[…] ulated for each gene and correction for multiple testing was again done using the FDR method. Post hoc power analyses for our TDT approach were carried out with the snpPower function in the R-package Haplin v6.0.1.To reduce the risk of type II errors, we attempted replication of our nominally significant (P value <0.05) SNPs against nominal significance of the case–control comparisons stemming fro […]

Citations

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Haplin institution(s)
Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway; Department of Genetics and Bioinformatics, Norwegian Institute of Public Health (NIPH), Oslo, Norway; Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway; Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences (NIH/NIEHS), Durham, NC, USA; Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, USA; Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Pediatrics, University of Iowa, Iowa City, IA, USA; Epidemiology Branch, National Institute of Environmental Health Sciences (NIH/ NIEHS), Durham, NC, USA; Department of Health Registries, Norwegian Institute of Public Health, Oslo, Norway
Haplin funding source(s)
Supported by the Bergen Medical Research Foundation, grant 807191; in part by the Intramural Program of the National Institute of Environmental Health Sciences, National Institutes of Health (NIH/ NIEHS); by NIH grant DE08559; and partly by the Research Council of Norway, project number 262700.

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