Literature DB >> 30505573

A System for an Accountable Data Analysis Process in R.

Jonathan Gelfond1, Martin Goros2, Brian Hernandez3, Alex Bokov4.   

Abstract

Efficiently producing transparent analyses may be difficult for beginners or tedious for the experienced. This implies a need for computing systems and environments that can efficiently satisfy reproducibility and accountability standards. To this end, we have developed a system, R package, and R Shiny application called adapr (Accountable Data Analysis Process in R) that is built on the principle of accountable units. An accountable unit is a data file (statistic, table or graphic) that can be associated with a provenance, meaning how it was created, when it was created and who created it, and this is similar to the 'verifiable computational results' (VCR) concept proposed by Gavish and Donoho. Both accountable units and VCRs are version controlled, sharable, and can be incorporated into a collaborative project. However, accountable units use file hashes and do not involve watermarking or public repositories like VCRs. Reproducing collaborative work may be highly complex, requiring repeating computations on multiple systems from multiple authors; however, determining the provenance of each unit is simpler, requiring only a search using file hashes and version control systems.

Entities:  

Year:  2018        PMID: 30505573      PMCID: PMC6261481     

Source DB:  PubMed          Journal:  R J        ISSN: 2073-4859            Impact factor:   3.984


  8 in total

1.  Authorship policies of scientific journals.

Authors:  David B Resnik; Ana M Tyler; Jennifer R Black; Grace Kissling
Journal:  J Med Ethics       Date:  2015-12-29       Impact factor: 2.903

Review 2.  Orchestrating high-throughput genomic analysis with Bioconductor.

Authors:  Wolfgang Huber; Vincent J Carey; Robert Gentleman; Simon Anders; Marc Carlson; Benilton S Carvalho; Hector Corrada Bravo; Sean Davis; Laurent Gatto; Thomas Girke; Raphael Gottardo; Florian Hahne; Kasper D Hansen; Rafael A Irizarry; Michael Lawrence; Michael I Love; James MacDonald; Valerie Obenchain; Andrzej K Oleś; Hervé Pagès; Alejandro Reyes; Paul Shannon; Gordon K Smyth; Dan Tenenbaum; Levi Waldron; Martin Morgan
Journal:  Nat Methods       Date:  2015-02       Impact factor: 28.547

3.  How to Tell the Truth with Statistics: The Case for Accountable Data Analyses in Team-based Science.

Authors:  Jonathan A L Gelfond; Craig M Klugman; Leah J Welty; Elizabeth Heitman; Christopher Louden; Brad H Pollock
Journal:  J Transl Med Epidemiol       Date:  2014

4.  Improving Initiation and Tracking of Research Projects at an Academic Health Center: A Case Study.

Authors:  Susanne Schmidt; Martin Goros; Helen M Parsons; Can Saygin; Hung-Da Wan; Paula K Shireman; Jonathan A L Gelfond
Journal:  Eval Health Prof       Date:  2016-09-20       Impact factor: 2.651

5.  The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud.

Authors:  Katherine Wolstencroft; Robert Haines; Donal Fellows; Alan Williams; David Withers; Stuart Owen; Stian Soiland-Reyes; Ian Dunlop; Aleksandra Nenadic; Paul Fisher; Jiten Bhagat; Khalid Belhajjame; Finn Bacall; Alex Hardisty; Abraham Nieva de la Hidalga; Maria P Balcazar Vargas; Shoaib Sufi; Carole Goble
Journal:  Nucleic Acids Res       Date:  2013-05-02       Impact factor: 16.971

6.  The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.

Authors:  Enis Afgan; Dannon Baker; Marius van den Beek; Daniel Blankenberg; Dave Bouvier; Martin Čech; John Chilton; Dave Clements; Nate Coraor; Carl Eberhard; Björn Grüning; Aysam Guerler; Jennifer Hillman-Jackson; Greg Von Kuster; Eric Rasche; Nicola Soranzo; Nitesh Turaga; James Taylor; Anton Nekrutenko; Jeremy Goecks
Journal:  Nucleic Acids Res       Date:  2016-05-02       Impact factor: 16.971

7.  An R package that automatically collects and archives details for reproducible computing.

Authors:  Zhifa Liu; Stan Pounds
Journal:  BMC Bioinformatics       Date:  2014-05-10       Impact factor: 3.169

8.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444

  8 in total
  5 in total

1.  Growth recovery lines: a specific indicator of child abuse and neglect?

Authors:  Lora R Spiller; Nancy D Kellogg; Maria-Gisela Mercado-Deane; Anthony I Zarka; Jonathan A L Gelfond
Journal:  Pediatr Radiol       Date:  2019-09-14

2.  Decreased plasma rifapentine concentrations associated with AADAC single nucleotide polymorphism in adults with tuberculosis.

Authors:  Marc Weiner; Jon Gelfond; Teresa L Johnson-Pais; Melissa Engle; John L Johnson; William C Whitworth; Erin Bliven-Sizemore; Pheona Nsubuga; Susan E Dorman; Rada Savic
Journal:  J Antimicrob Chemother       Date:  2021-02-11       Impact factor: 5.790

3.  Genetically heterogeneous mice exhibit a female survival advantage that is age- and site-specific: Results from a large multi-site study.

Authors:  Catherine J Cheng; Jonathan A L Gelfond; Randy Strong; James F Nelson
Journal:  Aging Cell       Date:  2019-02-23       Impact factor: 9.304

4.  Creating and sharing reproducible research code the workflowr way.

Authors:  John D Blischak; Peter Carbonetto; Matthew Stephens
Journal:  F1000Res       Date:  2019-10-14

5.  Mobilization-based transplantation of young-donor hematopoietic stem cells extends lifespan in mice.

Authors:  Michael J Guderyon; Cang Chen; Anindita Bhattacharjee; Guo Ge; Roman A Fernandez; Jonathan A L Gelfond; Karla M Gorena; Catherine J Cheng; Yang Li; James F Nelson; Randy J Strong; Peter J Hornsby; Robert A Clark; Senlin Li
Journal:  Aging Cell       Date:  2020-02-03       Impact factor: 9.304

  5 in total

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