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LDsnpR specifications

Information


Unique identifier OMICS_29663
Name LDsnpR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 0.5.0
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline Andrea Christoforou
  • person_outline LDsnpR Team

Additional information


http://services.cbu.uib.no/software/ldsnpr/Documentation

Publication for LDsnpR

LDsnpR citations

 (8)
library_books

Recently evolved human specific methylated regions are enriched in schizophrenia signals

2018
BMC Evol Biol
PMCID: 5946405
PMID: 29747567
DOI: 10.1186/s12862-018-1177-2

[…] SNPs were assigned to DMRs with LDsnpR [] using positional binning and LD (linkage disequilibrium)-based binning in R []. We used both methods because DMR-localized SNPs that were not genotyped in a specific GWAS would be missed if […]

library_books

Analysis of the joint effect of SNPs to identify independent loci and allelic heterogeneity in schizophrenia GWAS data

2017
PMCID: 5802566
PMID: 29249828
DOI: 10.1038/s41398-017-0033-2

[…] e new genomic loci associated with SCZ. The genomic loci were defined by the associated SNP and all SNPs in LD with the associated SNP (r 2 > 0.2). Gene annotations were performed with the aid of the LDsnpR package and the RefSeq gene list. […]

library_books

Interactome transcriptome analysis discovers signatures complementary to GWAS Loci of Type 2 Diabetes

2016
Sci Rep
PMCID: 5067504
PMID: 27752041
DOI: 10.1038/srep35228

[…] ion. We referred all T2D-associated genes deposited in GWAS Catalogue as T2D-GWAS genes and T2D genes reported by the DIAGRAM meta-analysis as DIAGRAM-genes.We used a LD-based SNP binning tool, named LDsnpR, to identify additional SNPs in the DIAGRAM-database which might be associated with T2D, targeted at the gene level. We assigned SNP marker information and p-values from the DIAGRAM-database to […]

library_books

Genetics of structural connectivity and information processing in the brain

2016
PMCID: 5102980
PMID: 26852023
DOI: 10.1007/s00429-016-1194-0

[…] f specific gene sets of interest are enriched for association in a GWAS. First, P values from the two meta-analyses were assigned to genes and used to calculate gene-based scores, using the R package LDsnpR (Christoforou et al. ) with ENSEMBL66 gene definitions (±10 kb). Since the datasets used were imputed at a high-density level, no additional LD parameters were included. Each ENSEMBL gene was t […]

library_books

Common variants in the ARC gene are not associated with cognitive abilities

2015
PMCID: 4614059
PMID: 26516611
DOI: 10.1002/brb3.376

[…] ibrium (HWE; exact test) P‐value <0.001. After quality control of the NCNG genotyping data, 645 individuals remained. The markers located in the ARC gene (+/−10 kb) or in LD were identified using the LDsnpR tool (Christoforou et al. ). This set consisted of two SNPs that were genotyped and 69 SNPs that were imputed. […]

library_books

A Genetic Deconstruction of Neurocognitive Traits in Schizophrenia and Bipolar Disorder

2013
PLoS One
PMCID: 3861303
PMID: 24349030
DOI: 10.1371/journal.pone.0081052

[…] he linkage disequilibrium (LD) of the genotyped SNPs with any other SNPs within the gene boundaries, based on the HapMap CEU reference sample . This gene-based binning of SNPs was performed using the LDsnpR package with the following parameters: the gene annotation used was the “Human Ensembl release 54” , the gene boundaries were set to 10kb upstream and downstream of the gene, the LD data used […]

Citations

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LDsnpR institution(s)
Dr. Einar Martens Research Group for Biological Psychiatry, Department of Clinical Medicine, University of Bergen, Bergen, Norway; Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway; Computational Biology Unit, Uni Computing, Uni Research, Bergen, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Research Unit, Sørlandet Hospital HF, Kristiansand, Norway; Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany; Institute of Human Genetics, University of Bonn, Bonn, Germany; Institute for Genomic Mathematics, University of Bonn, Bonn, Germany; Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; German Centre for Neurodegenerative Disorders, Bonn, Germany; Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, University of Mannheim, Mannheim, Germany; Structural and Functional Organization of the Brain, Institute of Neuroscience and Medicine, Research Center Julich, Julich, Germany; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Department of Informatics, University of Bergen, Bergen, Norway
LDsnpR funding source(s)
Supported by grants from the Bergen Research Foundation, the University of Bergen, the Research Council of Norway (FUGE, Psyksik Helse, and eVita), UNI Computing, Western Norway Regional Health Authority (Helse Vest), the Dr. Einar Martens Fund, South-Eastern Norway Regional Health Authority (Helse Sør-Øst), the National Institutes of Health and the National Heart, Lung, and Blood Institute (U01 HL089856, RO1 MH087590 and R01 MH081862), and the German Federal Ministry of Education and Research (National Genome Research Network 2, the National Genome Research Network plus, and the Integrated Genome Research Network MooDS [grant 01GS08144]).

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