Literature DB >> 23052040

GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies.

Stephanie M Gogarten1, Tushar Bhangale, Matthew P Conomos, Cecelia A Laurie, Caitlin P McHugh, Ian Painter, Xiuwen Zheng, David R Crosslin, David Levine, Thomas Lumley, Sarah C Nelson, Kenneth Rice, Jess Shen, Rohit Swarnkar, Bruce S Weir, Cathy C Laurie.   

Abstract

GWASTools is an R/Bioconductor package for quality control and analysis of genome-wide association studies (GWAS). GWASTools brings the interactive capability and extensive statistical libraries of R to GWAS. Data are stored in NetCDF format to accommodate extremely large datasets that cannot fit within R's memory limits. The documentation includes instructions for converting data from multiple formats, including variants called from sequencing. GWASTools provides a convenient interface for linking genotypes and intensity data with sample and single nucleotide polymorphism annotation.

Mesh：

Year:  2012        PMID： 23052040      PMCID： PMC3519456          DOI： 10.1093/bioinformatics/bts610

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  8 in total

1.  High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping.

Authors:  Daniel A Peiffer; Jennie M Le; Frank J Steemers; Weihua Chang; Tony Jenniges; Francisco Garcia; Kirt Haden; Jiangzhen Li; Chad A Shaw; John Belmont; Sau Wai Cheung; Richard M Shen; David L Barker; Kevin L Gunderson
Journal:  Genome Res       Date:  2006-08-09       Impact factor: 9.043

2.  A faster circular binary segmentation algorithm for the analysis of array CGH data.

Authors:  E S Venkatraman; Adam B Olshen
Journal:  Bioinformatics       Date:  2007-01-18       Impact factor: 6.937

3.  An R package for analysis of whole-genome association studies.

Authors:  David Clayton; Hin-Tak Leung
Journal:  Hum Hered       Date:  2007-04-27       Impact factor: 0.444

4.  A high-performance computing toolset for relatedness and principal component analysis of SNP data.

Authors:  Xiuwen Zheng; David Levine; Jess Shen; Stephanie M Gogarten; Cathy Laurie; Bruce S Weir
Journal:  Bioinformatics       Date:  2012-10-11       Impact factor: 6.937

5.  Quality control and quality assurance in genotypic data for genome-wide association studies.

Authors:  Cathy C Laurie; Kimberly F Doheny; Daniel B Mirel; Elizabeth W Pugh; Laura J Bierut; Tushar Bhangale; Frederick Boehm; Neil E Caporaso; Marilyn C Cornelis; Howard J Edenberg; Stacy B Gabriel; Emily L Harris; Frank B Hu; Kevin B Jacobs; Peter Kraft; Maria Teresa Landi; Thomas Lumley; Teri A Manolio; Caitlin McHugh; Ian Painter; Justin Paschall; John P Rice; Kenneth M Rice; Xiuwen Zheng; Bruce S Weir
Journal:  Genet Epidemiol       Date:  2010-09       Impact factor: 2.135

6.  Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis.

Authors:  Laura K Conlin; Brian D Thiel; Carsten G Bonnemann; Livija Medne; Linda M Ernst; Elaine H Zackai; Matthew A Deardorff; Ian D Krantz; Hakon Hakonarson; Nancy B Spinner
Journal:  Hum Mol Genet       Date:  2010-01-06       Impact factor: 6.150

7.  The Gene, Environment Association Studies consortium (GENEVA): maximizing the knowledge obtained from GWAS by collaboration across studies of multiple conditions.

Authors:  Marilyn C Cornelis; Arpana Agrawal; John W Cole; Nadia N Hansel; Kathleen C Barnes; Terri H Beaty; Siiri N Bennett; Laura J Bierut; Eric Boerwinkle; Kimberly F Doheny; Bjarke Feenstra; Eleanor Feingold; Myriam Fornage; Christopher A Haiman; Emily L Harris; M Geoffrey Hayes; John A Heit; Frank B Hu; Jae H Kang; Cathy C Laurie; Hua Ling; Teri A Manolio; Mary L Marazita; Rasika A Mathias; Daniel B Mirel; Justin Paschall; Louis R Pasquale; Elizabeth W Pugh; John P Rice; Jenna Udren; Rob M van Dam; Xiaojing Wang; Janey L Wiggs; Kayleen Williams; Kai Yu
Journal:  Genet Epidemiol       Date:  2010-05       Impact factor: 2.135

8.  Detectable clonal mosaicism from birth to old age and its relationship to cancer.

Authors:  Cathy C Laurie; Cecelia A Laurie; Kenneth Rice; Kimberly F Doheny; Leila R Zelnick; Caitlin P McHugh; Hua Ling; Kurt N Hetrick; Elizabeth W Pugh; Chris Amos; Qingyi Wei; Li-e Wang; Jeffrey E Lee; Kathleen C Barnes; Nadia N Hansel; Rasika Mathias; Denise Daley; Terri H Beaty; Alan F Scott; Ingo Ruczinski; Rob B Scharpf; Laura J Bierut; Sarah M Hartz; Maria Teresa Landi; Neal D Freedman; Lynn R Goldin; David Ginsburg; Jun Li; Karl C Desch; Sara S Strom; William J Blot; Lisa B Signorello; Sue A Ingles; Stephen J Chanock; Sonja I Berndt; Loic Le Marchand; Brian E Henderson; Kristine R Monroe; John A Heit; Mariza de Andrade; Sebastian M Armasu; Cynthia Regnier; William L Lowe; M Geoffrey Hayes; Mary L Marazita; Eleanor Feingold; Jeffrey C Murray; Mads Melbye; Bjarke Feenstra; Jae H Kang; Janey L Wiggs; Gail P Jarvik; Andrew N McDavid; Venkatraman E Seshan; Daniel B Mirel; Andrew Crenshaw; Nataliya Sharopova; Anastasia Wise; Jess Shen; David R Crosslin; David M Levine; Xiuwen Zheng; Jenna I Udren; Siiri Bennett; Sarah C Nelson; Stephanie M Gogarten; Matthew P Conomos; Patrick Heagerty; Teri Manolio; Louis R Pasquale; Christopher A Haiman; Neil Caporaso; Bruce S Weir
Journal:  Nat Genet       Date:  2012-05-06       Impact factor: 38.330
  8 in total
  78 in total

1.  PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers.

Authors:  Alejandro Q Nato; Nicola H Chapman; Harkirat K Sohi; Hiep D Nguyen; Zoran Brkanac; Ellen M Wijsman
Journal:  Bioinformatics       Date:  2015-07-30       Impact factor: 6.937

2.  Burden of potentially pathologic copy number variants is higher in children with isolated congenital heart disease and significantly impairs covariate-adjusted transplant-free survival.

Authors:  Daniel Seung Kim; Jerry H Kim; Amber A Burt; David R Crosslin; Nancy Burnham; Cecilia E Kim; Donna M McDonald-McGinn; Elaine H Zackai; Susan C Nicolson; Thomas L Spray; Ian B Stanaway; Deborah A Nickerson; Patrick J Heagerty; Hakon Hakonarson; J William Gaynor; Gail P Jarvik
Journal:  J Thorac Cardiovasc Surg       Date:  2015-11-10       Impact factor: 5.209

3.  Genetic Diversity and Association Studies in US Hispanic/Latino Populations: Applications in the Hispanic Community Health Study/Study of Latinos.

Authors:  Matthew P Conomos; Cecelia A Laurie; Adrienne M Stilp; Stephanie M Gogarten; Caitlin P McHugh; Sarah C Nelson; Tamar Sofer; Lindsay Fernández-Rhodes; Anne E Justice; Mariaelisa Graff; Kristin L Young; Amanda A Seyerle; Christy L Avery; Kent D Taylor; Jerome I Rotter; Gregory A Talavera; Martha L Daviglus; Sylvia Wassertheil-Smoller; Neil Schneiderman; Gerardo Heiss; Robert C Kaplan; Nora Franceschini; Alex P Reiner; John R Shaffer; R Graham Barr; Kathleen F Kerr; Sharon R Browning; Brian L Browning; Bruce S Weir; M Larissa Avilés-Santa; George J Papanicolaou; Thomas Lumley; Adam A Szpiro; Kari E North; Ken Rice; Timothy A Thornton; Cathy C Laurie
Journal:  Am J Hum Genet       Date:  2016-01-07       Impact factor: 11.025

4.  Quantifying realized inbreeding in wild and captive animal populations.

Authors:  U Knief; G Hemmrich-Stanisak; M Wittig; A Franke; S C Griffith; B Kempenaers; W Forstmeier
Journal:  Heredity (Edinb)       Date:  2015-01-14       Impact factor: 3.821

5.  The Summer Institute in Statistical Genetics.

Authors:  Bruce S Weir
Journal:  Genetics       Date:  2019-08       Impact factor: 4.562

6.  Genetic association testing using the GENESIS R/Bioconductor package.

Authors:  Stephanie M Gogarten; Tamar Sofer; Han Chen; Chaoyu Yu; Jennifer A Brody; Timothy A Thornton; Kenneth M Rice; Matthew P Conomos
Journal:  Bioinformatics       Date:  2019-12-15       Impact factor: 6.937

7.  Genome-Wide Association Study of Heavy Smoking and Daily/Nondaily Smoking in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).

Authors:  Nancy L Saccone; Leslie S Emery; Tamar Sofer; Stephanie M Gogarten; Diane M Becker; Erwin P Bottinger; Li-Shiun Chen; Robert C Culverhouse; Weimin Duan; Dana B Hancock; H Dean Hosgood; Eric O Johnson; Ruth J F Loos; Tin Louie; George Papanicolaou; Krista M Perreira; Erik J Rodriquez; Claudia Schurmann; Adrienne M Stilp; Adam A Szpiro; Gregory A Talavera; Kent D Taylor; James F Thrasher; Lisa R Yanek; Cathy C Laurie; Eliseo J Pérez-Stable; Laura J Bierut; Robert C Kaplan
Journal:  Nicotine Tob Res       Date:  2018-03-06       Impact factor: 4.244

8.  gwasurvivr: an R package for genome-wide survival analysis.

Authors:  Abbas A Rizvi; Ezgi Karaesmen; Martin Morgan; Leah Preus; Junke Wang; Michael Sovic; Theresa Hahn; Lara E Sucheston-Campbell
Journal:  Bioinformatics       Date:  2019-06-01       Impact factor: 6.937

9.  Protocols, Methods, and Tools for Genome-Wide Association Studies (GWAS) of Dental Traits.

Authors:  Cary S Agler; Dmitry Shungin; Andrea G Ferreira Zandoná; Paige Schmadeke; Patricia V Basta; Jason Luo; John Cantrell; Thomas D Pahel; Beau D Meyer; John R Shaffer; Arne S Schaefer; Kari E North; Kimon Divaris
Journal:  Methods Mol Biol       Date:  2019

10.  Genomic analyses in African populations identify novel risk loci for cleft palate.

Authors:  Azeez Butali; Peter A Mossey; Wasiu L Adeyemo; Mekonen A Eshete; Lord J J Gowans; Tamara D Busch; Deepti Jain; Wenjie Yu; Liu Huan; Cecelia A Laurie; Cathy C Laurie; Sarah Nelson; Mary Li; Pedro A Sanchez-Lara; William P Magee; Kathleen S Magee; Allyn Auslander; Frederick Brindopke; Denise M Kay; Michele Caggana; Paul A Romitti; James L Mills; Rosemary Audu; Chika Onwuamah; Ganiyu O Oseni; Arwa Owais; Olutayo James; Peter B Olaitan; Babatunde S Aregbesola; Ramat O Braimah; Fadekemi O Oginni; Ayodeji O Oladele; Saidu A Bello; Jennifer Rhodes; Rita Shiang; Peter Donkor; Solomon Obiri-Yeboah; Fareed Kow Nanse Arthur; Peter Twumasi; Pius Agbenorku; Gyikua Plange-Rhule; Alexander Acheampong Oti; Olugbenga M Ogunlewe; Afisu A Oladega; Adegbayi A Adekunle; Akinwunmi O Erinoso; Olatunbosun O Adamson; Abosede A Elufowoju; Oluwanifemi I Ayelomi; Taiye Hailu; Abiye Hailu; Yohannes Demissie; Miliard Derebew; Steve Eliason; Miguel Romero-Bustillous; Cynthia Lo; James Park; Shaan Desai; Muiawa Mohammed; Firke Abate; Lukman O Abdur-Rahman; Deepti Anand; Irfaan Saadi; Abimibola V Oladugba; Salil A Lachke; Brad A Amendt; Charles N Rotimi; Mary L Marazita; Robert A Cornell; Jeffrey C Murray; Adebowale A Adeyemo
Journal:  Hum Mol Genet       Date:  2019-03-15       Impact factor: 6.150
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