Literature DB >> 28172529

Assocplots: a Python package for static and interactive visualization of multiple-group GWAS results.

Ekaterina A Khramtsova1,2, Barbara E Stranger1,2,3.   

Abstract

Background: Over the last decade, genome-wide association studies (GWAS) have generated vast amounts of analysis results, requiring development of novel tools for data visualization. Quantile–quantile (QQ) plots and Manhattan plots are classical tools which have been utilized to visually summarize GWAS results and identify genetic variants significantly associated with traits of interest. However, static visualizations are limiting in the information that can be shown. Here, we present Assocplots, a Python package for viewing and exploring GWAS results not only using classic static Manhattan and QQ plots, but also through a dynamic extension which allows to interactively visualize the relationships between GWAS results from multiple cohorts or studies. Availability and Implementation: The Assocplots package is open source and distributed under the MIT license via GitHub (https://github.com/khramts/assocplots) along with examples, documentation and installation instructions. Contact: ekhramts@medicine.bsd.uchicago.edu or bstranger@medicine.bsd.uchicago.edu

Mesh：

Year:  2017        PMID： 28172529      PMCID： PMC6410886          DOI： 10.1093/bioinformatics/btw641

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


  6 in total

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Authors:  Mitchell J Machiela; Stephen J Chanock
Journal:  Bioinformatics       Date:  2015-07-02       Impact factor: 6.937

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Journal:  Bioinformatics       Date:  2010-07-15       Impact factor: 6.937

5.  R/qtlcharts: interactive graphics for quantitative trait locus mapping.

Authors:  Karl W Broman
Journal:  Genetics       Date:  2014-12-18       Impact factor: 4.562

6.  Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits.

Authors:  Joshua C Randall; Thomas W Winkler; Zoltán Kutalik; Sonja I Berndt; Anne U Jackson; Keri L Monda; Tuomas O Kilpeläinen; Tõnu Esko; Reedik Mägi; Shengxu Li; Tsegaselassie Workalemahu; Mary F Feitosa; Damien C Croteau-Chonka; Felix R Day; Tove Fall; Teresa Ferreira; Stefan Gustafsson; Adam E Locke; Iain Mathieson; Andre Scherag; Sailaja Vedantam; Andrew R Wood; Liming Liang; Valgerdur Steinthorsdottir; Gudmar Thorleifsson; Emmanouil T Dermitzakis; Antigone S Dimas; Fredrik Karpe; Josine L Min; George Nicholson; Deborah J Clegg; Thomas Person; Jon P Krohn; Sabrina Bauer; Christa Buechler; Kristina Eisinger; Amélie Bonnefond; Philippe Froguel; Jouke-Jan Hottenga; Inga Prokopenko; Lindsay L Waite; Tamara B Harris; Albert Vernon Smith; Alan R Shuldiner; Wendy L McArdle; Mark J Caulfield; Patricia B Munroe; Henrik Grönberg; Yii-Der Ida Chen; Guo Li; Jacques S Beckmann; Toby Johnson; Unnur Thorsteinsdottir; Maris Teder-Laving; Kay-Tee Khaw; Nicholas J Wareham; Jing Hua Zhao; Najaf Amin; Ben A Oostra; Aldi T Kraja; Michael A Province; L Adrienne Cupples; Nancy L Heard-Costa; Jaakko Kaprio; Samuli Ripatti; Ida Surakka; Francis S Collins; Jouko Saramies; Jaakko Tuomilehto; Antti Jula; Veikko Salomaa; Jeanette Erdmann; Christian Hengstenberg; Christina Loley; Heribert Schunkert; Claudia Lamina; H Erich Wichmann; Eva Albrecht; Christian Gieger; Andrew A Hicks; Asa Johansson; Peter P Pramstaller; Sekar Kathiresan; Elizabeth K Speliotes; Brenda Penninx; Anna-Liisa Hartikainen; Marjo-Riitta Jarvelin; Ulf Gyllensten; Dorret I Boomsma; Harry Campbell; James F Wilson; Stephen J Chanock; Martin Farrall; Anuj Goel; Carolina Medina-Gomez; Fernando Rivadeneira; Karol Estrada; André G Uitterlinden; Albert Hofman; M Carola Zillikens; Martin den Heijer; Lambertus A Kiemeney; Andrea Maschio; Per Hall; Jonathan Tyrer; Alexander Teumer; Henry Völzke; Peter Kovacs; Anke Tönjes; Massimo Mangino; Tim D Spector; Caroline Hayward; Igor Rudan; Alistair S Hall; Nilesh J Samani; Antony Paul Attwood; Jennifer G Sambrook; Joseph Hung; Lyle J Palmer; Marja-Liisa Lokki; Juha Sinisalo; Gabrielle Boucher; Heikki Huikuri; Mattias Lorentzon; Claes Ohlsson; Niina Eklund; Johan G Eriksson; Cristina Barlassina; Carlo Rivolta; Ilja M Nolte; Harold Snieder; Melanie M Van der Klauw; Jana V Van Vliet-Ostaptchouk; Pablo V Gejman; Jianxin Shi; Kevin B Jacobs; Zhaoming Wang; Stephan J L Bakker; Irene Mateo Leach; Gerjan Navis; Pim van der Harst; Nicholas G Martin; Sarah E Medland; Grant W Montgomery; Jian Yang; Daniel I Chasman; Paul M Ridker; Lynda M Rose; Terho Lehtimäki; Olli Raitakari; Devin Absher; Carlos Iribarren; Hanneke Basart; Kees G Hovingh; Elina Hyppönen; Chris Power; Denise Anderson; John P Beilby; Jennie Hui; Jennifer Jolley; Hendrik Sager; Stefan R Bornstein; Peter E H Schwarz; Kati Kristiansson; Markus Perola; Jaana Lindström; Amy J Swift; Matti Uusitupa; Mustafa Atalay; Timo A Lakka; Rainer Rauramaa; Jennifer L Bolton; Gerry Fowkes; Ross M Fraser; Jackie F Price; Krista Fischer; Kaarel Krjutå Kov; Andres Metspalu; Evelin Mihailov; Claudia Langenberg; Jian'an Luan; Ken K Ong; Peter S Chines; Sirkka M Keinanen-Kiukaanniemi; Timo E Saaristo; Sarah Edkins; Paul W Franks; Göran Hallmans; Dmitry Shungin; Andrew David Morris; Colin N A Palmer; Raimund Erbel; Susanne Moebus; Markus M Nöthen; Sonali Pechlivanis; Kristian Hveem; Narisu Narisu; Anders Hamsten; Steve E Humphries; Rona J Strawbridge; Elena Tremoli; Harald Grallert; Barbara Thorand; Thomas Illig; Wolfgang Koenig; Martina Müller-Nurasyid; Annette Peters; Bernhard O Boehm; Marcus E Kleber; Winfried März; Bernhard R Winkelmann; Johanna Kuusisto; Markku Laakso; Dominique Arveiler; Giancarlo Cesana; Kari Kuulasmaa; Jarmo Virtamo; John W G Yarnell; Diana Kuh; Andrew Wong; Lars Lind; Ulf de Faire; Bruna Gigante; Patrik K E Magnusson; Nancy L Pedersen; George Dedoussis; Maria Dimitriou; Genovefa Kolovou; Stavroula Kanoni; Kathleen Stirrups; Lori L Bonnycastle; Inger Njølstad; Tom Wilsgaard; Andrea Ganna; Emil Rehnberg; Aroon Hingorani; Mika Kivimaki; Meena Kumari; Themistocles L Assimes; Inês Barroso; Michael Boehnke; Ingrid B Borecki; Panos Deloukas; Caroline S Fox; Timothy Frayling; Leif C Groop; Talin Haritunians; David Hunter; Erik Ingelsson; Robert Kaplan; Karen L Mohlke; Jeffrey R O'Connell; David Schlessinger; David P Strachan; Kari Stefansson; Cornelia M van Duijn; Gonçalo R Abecasis; Mark I McCarthy; Joel N Hirschhorn; Lu Qi; Ruth J F Loos; Cecilia M Lindgren; Kari E North; Iris M Heid
Journal:  PLoS Genet       Date:  2013-06-06       Impact factor: 5.917
  6 in total
  7 in total

1.  JASS: command line and web interface for the joint analysis of GWAS results.

Authors:  Hanna Julienne; Pierre Lechat; Vincent Guillemot; Carla Lasry; Chunzi Yao; Robinson Araud; Vincent Laville; Bjarni Vilhjalmsson; Hervé Ménager; Hugues Aschard
Journal:  NAR Genom Bioinform       Date:  2020-01-24

2.  Sex differences in the genetic architecture of obsessive-compulsive disorder.

Authors:  Ekaterina A Khramtsova; Raphael Heldman; Eske M Derks; Dongmei Yu; Lea K Davis; Barbara E Stranger
Journal:  Am J Med Genet B Neuropsychiatr Genet       Date:  2018-11-20       Impact factor: 3.568

3.  Revealing the complex genetic architecture of obsessive-compulsive disorder using meta-analysis.

Authors: 
Journal:  Mol Psychiatry       Date:  2017-08-01       Impact factor: 15.992

4.  BigTop: a three-dimensional virtual reality tool for GWAS visualization.

Authors:  Samuel T Westreich; Maria Nattestad; Christopher Meyer
Journal:  BMC Bioinformatics       Date:  2020-01-31       Impact factor: 3.169

5.  flashfm-ivis: interactive visualisation for fine-mapping of multiple quantitative traits.

Authors:  Feng Zhou; Adam S Butterworth; Jennifer L Asimit
Journal:  Bioinformatics       Date:  2022-07-06       Impact factor: 6.931

6.  IntAssoPlot: An R Package for Integrated Visualization of Genome-Wide Association Study Results With Gene Structure and Linkage Disequilibrium Matrix.

Authors:  Fengyu He; Shuangcheng Ding; Hongwei Wang; Feng Qin
Journal:  Front Genet       Date:  2020-03-20       Impact factor: 4.599

7.  PheGWAS: a new dimension to visualize GWAS across multiple phenotypes.

Authors:  Gittu George; Sushrima Gan; Yu Huang; Philip Appleby; A S Nar; Radha Venkatesan; Viswanathan Mohan; Colin N A Palmer; Alex S F Doney
Journal:  Bioinformatics       Date:  2020-04-15       Impact factor: 6.937
  7 in total

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