gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 11 2019
01 11 2019
Historique:
received:
03
12
2018
revised:
30
03
2019
accepted:
25
04
2019
pubmed:
10
5
2019
medline:
1
7
2020
entrez:
10
5
2019
Statut:
ppublish
Résumé
For the analysis of high-throughput genomic data produced by next-generation sequencing (NGS) technologies, researchers need to identify linkage disequilibrium (LD) structure in the genome. In this work, we developed an R package gpart which provides clustering algorithms to define LD blocks or analysis units consisting of SNPs. The visualization tool in gpart can display the LD structure and gene positions for up to 20 000 SNPs in one image. The gpart functions facilitate construction of LD blocks and SNP partitions for vast amounts of genome sequencing data within reasonable time and memory limits in personal computing environments. The R package is available at https://bioconductor.org/packages/gpart. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 31070701
pii: 5487391
doi: 10.1093/bioinformatics/btz308
pmc: PMC6821423
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4419-4421Subventions
Organisme : CIHR
ID : MOP-84287
Pays : Canada
Organisme : CIHR
ID : PJT 159463
Pays : Canada
Organisme : CIHR
ID : GET-101831
Pays : Canada
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press.
Références
Bioinformatics. 2018 Feb 1;34(3):388-397
pubmed: 29028986
Am J Hum Genet. 2002 Nov;71(5):1227-34
pubmed: 12384857
Science. 2002 Jun 21;296(5576):2225-9
pubmed: 12029063
BMC Bioinformatics. 2014 Jan 14;15:10
pubmed: 24423111
Bioinformatics. 2003 Jul 1;19(10):1300-1
pubmed: 12835279
Proc Natl Acad Sci U S A. 2002 May 28;99(11):7335-9
pubmed: 12032283
BMC Genomics. 2008 Aug 29;9:405
pubmed: 18759977
Trends Genet. 2013 Jan;29(1):23-30
pubmed: 23103023
Diabetologia. 2018 May;61(5):1098-1111
pubmed: 29404672
Bioinformatics. 2005 Jan 15;21(2):263-5
pubmed: 15297300
IEEE/ACM Trans Comput Biol Bioinform. 2016 Mar-Apr;13(2):315-25
pubmed: 27045830