Literature DB >> 19852806

SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel.

Bowang Chen1, Stefan Wilkening, Marion Drechsel, Kari Hemminki.   

Abstract

BACKGROUND: Single nucleotide polymorphism (SNP) genotyping is a major activity in biomedical research. Scientists prefer to have a facile access to the results which may require conversions between data formats. First hand SNP data is often entered in or saved in the MS-Excel format, but this software lacks genetic and epidemiological related functions. A general tool to do basic genetic and epidemiological analysis and data conversion for MS-Excel is needed.
FINDINGS: The SNP_tools package is prepared as an add-in for MS-Excel. The code is written in Visual Basic for Application, embedded in the Microsoft Office package. This add-in is an easy to use tool for users with basic computer knowledge (and requirements for basic statistical analysis).
CONCLUSION: Our implementation for Microsoft Excel 2000-2007 in Microsoft Windows 2000, XP, Vista and Windows 7 beta can handle files in different formats and converts them into other formats. It is a free software.

Entities:  

Year:  2009        PMID: 19852806      PMCID: PMC2771038          DOI: 10.1186/1756-0500-2-214

Source DB:  PubMed          Journal:  BMC Res Notes        ISSN: 1756-0500


  7 in total

1.  Merlin--rapid analysis of dense genetic maps using sparse gene flow trees.

Authors:  Gonçalo R Abecasis; Stacey S Cherny; William O Cookson; Lon R Cardon
Journal:  Nat Genet       Date:  2001-12-03       Impact factor: 38.330

2.  Haploview: analysis and visualization of LD and haplotype maps.

Authors:  J C Barrett; B Fry; J Maller; M J Daly
Journal:  Bioinformatics       Date:  2004-08-05       Impact factor: 6.937

3.  Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation.

Authors:  Matthew Stephens; Paul Scheet
Journal:  Am J Hum Genet       Date:  2005-01-31       Impact factor: 11.025

4.  LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage.

Authors:  K Hao; X Di; S Cawley
Journal:  Bioinformatics       Date:  2006-12-05       Impact factor: 6.937

5.  SNPassoc: an R package to perform whole genome association studies.

Authors:  Juan R González; Lluís Armengol; Xavier Solé; Elisabet Guinó; Josep M Mercader; Xavier Estivill; Víctor Moreno
Journal:  Bioinformatics       Date:  2007-01-31       Impact factor: 6.937

6.  A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase.

Authors:  Paul Scheet; Matthew Stephens
Journal:  Am J Hum Genet       Date:  2006-02-17       Impact factor: 11.025

7.  PLINK: a tool set for whole-genome association and population-based linkage analyses.

Authors:  Shaun Purcell; Benjamin Neale; Kathe Todd-Brown; Lori Thomas; Manuel A R Ferreira; David Bender; Julian Maller; Pamela Sklar; Paul I W de Bakker; Mark J Daly; Pak C Sham
Journal:  Am J Hum Genet       Date:  2007-07-25       Impact factor: 11.025

  7 in total
  23 in total

1.  A comprehensive study of polymorphisms in the ABCB1, ABCC2, ABCG2, NR1I2 genes and lymphoma risk.

Authors:  Daniele Campa; Katja Butterbach; Susan L Slager; Christine F Skibola; Silvia de Sanjosé; Yolanda Benavente; Nikolaus Becker; Lenka Foretova; Marc Maynadie; Pierluigi Cocco; Anthony Staines; Rudolf Kaaks; Paolo Boffetta; Paul Brennan; Lucia Conde; Paige M Bracci; Neil E Caporaso; Sara S Strom; Nicola J Camp; James R Cerhan; Federico Canzian; Alexandra Nieters
Journal:  Int J Cancer       Date:  2011-11-28       Impact factor: 7.396

2.  Genetic polymorphisms associated with breast cancer in malaysian cohort.

Authors:  Jagdish Kaur Chahil; Khamsigan Munretnam; Nurulhafizah Samsudin; Say Hean Lye; Nikman Adli Nor Hashim; Nurul Hanis Ramzi; Sharmila Velapasamy; Ler Lian Wee; Livy Alex
Journal:  Indian J Clin Biochem       Date:  2014-01-23

3.  Association of genetic and non-genetic risk factors with the development of prostate cancer in Malaysian men.

Authors:  Khamsigan Munretnam; Livy Alex; Nurul Hanis Ramzi; Jagdish Kaur Chahil; I S Kavitha; Nikman Adli Nor Hashim; Say Hean Lye; Sharmila Velapasamy; Lian Wee Ler
Journal:  Mol Biol Rep       Date:  2014-01-18       Impact factor: 2.316

4.  Evolutionary and polymorphism analyses reveal the central role of BTN3A2 in the concerted evolution of the BTN3 gene family.

Authors:  Hassnae Afrache; Pierre Pontarotti; Laurent Abi-Rached; Daniel Olive
Journal:  Immunogenetics       Date:  2017-04-05       Impact factor: 2.846

5.  Risk of advanced gastric precancerous lesions in Helicobacter pylori infected subjects is influenced by ABO blood group and cagA status.

Authors:  Cosmeri Rizzato; Ikuko Kato; Martyn Plummer; Nubia Muñoz; Angelika Stein; Leen Jan van Doorn; Silvia Franceschi; Federico Canzian
Journal:  Int J Cancer       Date:  2013-02-12       Impact factor: 7.396

6.  Polymorphisms in Host Immunity-Modulating Genes and Risk of Invasive Aspergillosis: Results from the AspBIOmics Consortium.

Authors:  C B Lupiañez; L M Canet; A Carvalho; L Alcazar-Fuoli; J Springer; M Lackner; J Segura-Catena; A Comino; C Olmedo; R Ríos; A Fernández-Montoya; M Cuenca-Estrella; C Solano; M Á López-Nevot; C Cunha; A Oliveira-Coelho; T Villaescusa; L Fianchi; J M Aguado; L Pagano; E López-Fernández; L Potenza; M Luppi; C Lass-Flörl; J Loeffler; H Einsele; L Vazquez; M Jurado; J Sainz
Journal:  Infect Immun       Date:  2015-12-14       Impact factor: 3.441

7.  Common genetic variants are associated with accelerated bone mineral density loss after hematopoietic cell transplantation.

Authors:  Song Yao; Lara E Sucheston; Shannon L Smiley; Warren Davis; Jeffrey M Conroy; Norma J Nowak; Christine B Ambrosone; Philip L McCarthy; Theresa Hahn
Journal:  PLoS One       Date:  2011-10-14       Impact factor: 3.240

8.  Genetic modifiers of menopausal hormone replacement therapy and breast cancer risk: a genome-wide interaction study.

Authors:  Anja Rudolph; Rebecca Hein; Sara Lindström; Lars Beckmann; Sabine Behrens; Jianjun Liu; Hugues Aschard; Manjeet K Bolla; Jean Wang; Thérèse Truong; Emilie Cordina-Duverger; Florence Menegaux; Thomas Brüning; Volker Harth; Gianluca Severi; Laura Baglietto; Melissa Southey; Stephen J Chanock; Jolanta Lissowska; Jonine D Figueroa; Mikael Eriksson; Keith Humpreys; Hatef Darabi; Janet E Olson; Kristen N Stevens; Celine M Vachon; Julia A Knight; Gord Glendon; Anna Marie Mulligan; Alan Ashworth; Nicholas Orr; Minouk Schoemaker; Penny M Webb; Pascal Guénel; Hiltrud Brauch; Graham Giles; Montserrat García-Closas; Kamila Czene; Georgia Chenevix-Trench; Fergus J Couch; Irene L Andrulis; Anthony Swerdlow; David J Hunter; Dieter Flesch-Janys; Douglas F Easton; Per Hall; Heli Nevanlinna; Peter Kraft; Jenny Chang-Claude
Journal:  Endocr Relat Cancer       Date:  2013-11-04       Impact factor: 5.678

9.  Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine.

Authors:  Ting-Yu Yeh; Gregory P Contreras
Journal:  Bull World Health Organ       Date:  2021-04-30       Impact factor: 9.408

10.  Bitter taste receptor polymorphisms and human aging.

Authors:  Daniele Campa; Francesco De Rango; Maura Carrai; Paolina Crocco; Alberto Montesanto; Federico Canzian; Giuseppina Rose; Cosmeri Rizzato; Giuseppe Passarino; Roberto Barale
Journal:  PLoS One       Date:  2012-11-02       Impact factor: 3.240

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