Cargando…

Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration

BACKGROUND: To gain statistical power or to allow fine mapping, researchers typically want to pool data before meta-analyses or genotype imputation. However, the necessary harmonization of genetic datasets is currently error-prone because of many different file formats and lack of clarity about whic...

Descripción completa

Detalles Bibliográficos
Autores principales:	Deelen, Patrick, Bonder, Marc Jan, van der Velde, K Joeri, Westra, Harm-Jan, Winder, Erwin, Hendriksen, Dennis, Franke, Lude, Swertz, Morris A
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2014
Materias:	Technical Note
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4307387/ https://www.ncbi.nlm.nih.gov/pubmed/25495213 http://dx.doi.org/10.1186/1756-0500-7-901

Ejemplares similares

Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels
por: Deelen, Patrick, et al.
Publicado: (2015)

reGenotyper: Detecting mislabeled samples in genetic data
por: Zych, Konrad, et al.
Publicado: (2017)

MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks
por: Pang, Chao, et al.
Publicado: (2016)

Single-cell RNA sequencing identifies cell type-specific cis-eQTLs and co-expression QTLs
por: van der Wijst, Monique G.P., et al.
Publicado: (2018)

Complex nature of SNP genotype effects on gene expression in primary human leucocytes
por: Heap, Graham A, et al.
Publicado: (2009)

An integrative approach for building personalized gene regulatory networks for precision medicine
por: van der Wijst, Monique G. P., et al.
Publicado: (2018)

Semi-automatic translation of medicine usage data (in Dutch, free-text) from Lifelines COVID-19 questionnaires to ATC codes
por: Kellmann, Alexander J, et al.
Publicado: (2023)

An integrative systems genetics approach reveals potential causal genes and pathways related to obesity
por: Kogelman, Lisette J. A., et al.
Publicado: (2015)

Feasibility of predicting allele specific expression from DNA sequencing using machine learning
por: Zhang, Zhenhua, et al.
Publicado: (2021)

MOLGENIS/OMX for multi-omics and personalized medicine
por: Swertz, Morris, et al.
Publicado: (2015)

Correction for both common and rare cell types in blood is important to identify genes that correlate with age
por: Pellegrino-Coppola, Damiano, et al.
Publicado: (2021)

BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing
por: Pang, Chao, et al.
Publicado: (2015)

Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response
por: de Vries, Dylan H., et al.
Publicado: (2020)

Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure
por: Oelen, Roy, et al.
Publicado: (2022)

InvertypeR: Bayesian inversion genotyping with Strand-seq data
por: Hanlon, Vincent C. T., et al.
Publicado: (2021)

Effects of spaced k-mers on alignment-free genotyping
por: Häntze, Hartmut, et al.
Publicado: (2023)

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments
por: Swertz, Morris A, et al.
Publicado: (2010)

A pipeline‐friendly software tool for genome diagnostics to prioritize genes by matching patient symptoms to literature
por: van der Velde, K. Joeri, et al.
Publicado: (2020)

Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data
por: Li, Shuang, et al.
Publicado: (2023)

Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores
por: Warmerdam, Robert, et al.
Publicado: (2021)

Clustering and Alignment of Polymorphic Sequences for HLA-DRB1 Genotyping
por: Ringquist, Steven, et al.
Publicado: (2013)

Current software for genotype imputation
por: Ellinghaus, David, et al.
Publicado: (2009)

Automatic and Rapid Discrimination of Cotton Genotypes by Near Infrared Spectroscopy and Chemometrics
por: Cui, Hai-Feng, et al.
Publicado: (2012)

Elucidating the genotype–phenotype map by automatic enumeration and analysis of the phenotypic repertoire
por: Lomnitz, Jason G, et al.
Publicado: (2015)

Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant
por: Almeida, Rodrigo, et al.
Publicado: (2014)

Automatic assessment of alignment quality
por: Lassmann, Timo, et al.
Publicado: (2005)

Worm variation made accessible: Take your shopping cart to store, link, and investigate!
por: Snoek, L Basten, et al.
Publicado: (2014)

T-ARMS PCR genotyping of SNP rs445709131 using thermostable strand displacement polymerase
por: Alyethodi, Rafeeque R., et al.
Publicado: (2018)

SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes
por: Krueger, Felix, et al.
Publicado: (2016)

KAGE: fast alignment-free graph-based genotyping of SNPs and short indels
por: Grytten, Ivar, et al.
Publicado: (2022)

Interleukin-1 Genotype in Periodontitis
por: Brodzikowska, Aniela, et al.
Publicado: (2019)

GAVIN: Gene-Aware Variant INterpretation for medical sequencing
por: van der Velde, K. Joeri, et al.
Publicado: (2017)

Lack of Association Between Genetic Variants at ACE2 and TMPRSS2 Genes Involved in SARS-CoV-2 Infection and Human Quantitative Phenotypes
por: Lopera Maya, Esteban A., et al.
Publicado: (2020)

Action-Depicting Gestures and Morphosyntax: The Function of Gesture-Speech Alignment in the Conversational Turn
por: Urbanik, Paweł, et al.
Publicado: (2021)

Identification of Superior Barley Genotypes Using Selection Index of Ideal Genotype (SIIG)
por: Zali, Hassan, et al.
Publicado: (2023)

Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands'
por: Deelen, Patrick, et al.
Publicado: (2014)

Analyzing metabolomics data for association with genotypes using two-component Gaussian mixture distributions
por: Westra, Jason, et al.
Publicado: (2018)

Automatic Tooth Segmentation of Dental Mesh Based on Harmonic Fields
por: Liao, Sheng-hui, et al.
Publicado: (2015)

SNPflow: A Lightweight Application for the Processing, Storing and Automatic Quality Checking of Genotyping Assays
por: Weissensteiner, Hansi, et al.
Publicado: (2013)

Automatic block-wise genotype-phenotype association detection based on hidden Markov model
por: Du, Jin, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_0ebaadal3l3uk934p8upukmavm