book.bib

@Manual{rmarkdown2021,
  title = {rmarkdown: Dynamic Documents for R},
  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
  year = {2021},
  note = {R package version 2.10},
  url = {https://github.com/rstudio/rmarkdown},
}

@Book{Xie2018,
  title = {R Markdown: The Definitive Guide},
  author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2018},
  note = {ISBN 9781138359338},
  url = {https://bookdown.org/yihui/rmarkdown},
}

@Book{Xie2020,
  title = {R Markdown Cookbook},
  author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2020},
  note = {ISBN 9780367563837},
  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
}

@Manual{rmarkdown2021,
  title = {rmarkdown: Dynamic Documents for R},
  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
  year = {2021},
  note = {R package version 2.10},
  url = {https://github.com/rstudio/rmarkdown},
}

@Book{Xie2018,
  title = {R Markdown: The Definitive Guide},
  author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2018},
  note = {ISBN 9781138359338},
  url = {https://bookdown.org/yihui/rmarkdown},
}

@Book{Xie2020,
  title = {R Markdown Cookbook},
  author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2020},
  note = {ISBN 9780367563837},
  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
}




@article{bauchner_citation_2016,
    author = {Bauchner, Howard and Golub, Robert M. and Fontanarosa, Phil B.},
    title = "{Data Sharing: An Ethical and Scientific Imperative}",
    journal = {JAMA},
    volume = {315},
    number = {12},
    pages = {1238-1240},
    year = {2016},
    month = {03},
    issn = {0098-7484},
    doi = {10.1001/jama.2016.2420},
    url = {https://doi.org/10.1001/jama.2016.2420},
    eprint = {https://jamanetwork.com/journals/jama/articlepdf/2504790/jed160017.pdf},
}

@article{bonomi_citation_2020,
	author = {Bonomi, Luca and Huang, Yingxiang and Ohno-Machado, Lucila},
	date = {2020/07/01},
	date-added = {2022-10-26 09:20:24 -0400},
	date-modified = {2022-10-26 09:20:24 -0400},
	doi = {10.1038/s41588-020-0651-0},
	id = {Bonomi2020},
	isbn = {1546-1718},
	journal = {Nature Genetics},
	number = {7},
	pages = {646--654},
	title = {Privacy challenges and research opportunities for genomic data sharing},
	url = {https://doi.org/10.1038/s41588-020-0651-0},
	volume = {52},
	year = {2020},
	bdsk-url-1 = {https://doi.org/10.1038/s41588-020-0651-0}
}

@article{colavizza_citation_2020,
	title = {The citation advantage of linking publications to research data},
	volume = {15},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0230416},
	doi = {10.1371/journal.pone.0230416},
	abstract = {Efforts to make research results open and reproducible are increasingly reflected by journal policies encouraging or mandating authors to provide data availability statements. As a consequence of this, there has been a strong uptake of data availability statements in recent literature. Nevertheless, it is still unclear what proportion of these statements actually contain well-formed links to data, for example via a URL or permanent identifier, and if there is an added value in providing such links. We consider 531, 889 journal articles published by PLOS and BMC, develop an automatic system for labelling their data availability statements according to four categories based on their content and the type of data availability they display, and finally analyze the citation advantage of different statement categories via regression. We find that, following mandated publisher policies, data availability statements become very common. In 2018 93.7\% of 21,793 PLOS articles and 88.2\% of 31,956 BMC articles had data availability statements. Data availability statements containing a link to data in a repository—rather than being available on request or included as supporting information files—are a fraction of the total. In 2017 and 2018, 20.8\% of PLOS publications and 12.2\% of BMC publications provided DAS containing a link to data in a repository. We also find an association between articles that include statements that link to data in a repository and up to 25.36\% (± 1.07\%) higher citation impact on average, using a citation prediction model. We discuss the potential implications of these results for authors (researchers) and journal publishers who make the effort of sharing their data in repositories. All our data and code are made available in order to reproduce and extend our results.},
	language = {en},
	number = {4},
	urldate = {2022-10-19},
	journal = {PLOS ONE},
	author = {Colavizza, Giovanni and Hrynaszkiewicz, Iain and Staden, Isla and Whitaker, Kirstie and McGillivray, Barbara},
	month = apr,
	year = {2020},
	note = {Publisher: Public Library of Science},
	keywords = {Bibliometrics, Citation analysis, Data management, Open access publishing, Reproducibility, Science policy, Scientific publishing, Support vector machines},
	pages = {e0230416},
	annote = {justified},
}

@article{cosgriff_citation_2020,
	title = {Data sharing in the era of {COVID}-19},
	volume = {2},
	issn = {2589-7500},
	url = {https://doi.org/10.1016/S2589-7500(20)30082-0},
	doi = {10.1016/S2589-7500(20)30082-0},
	number = {5},
	urldate = {2022-10-26},
	journal = {The Lancet Digital Health},
	author = {Cosgriff, Christopher V and Ebner, Daniel K and Celi, Leo Anthony},
	month = may,
	year = {2020},
	note = {Publisher: Elsevier},
	pages = {e224},
	annote = {doi: 10.1016/S2589-7500(20)30082-0},
}

@article {mckiernan_citation_2016,
  article_type = {journal},
  title = {Point of View: How open science helps researchers succeed},
  author = {McKiernan, Erin C and Bourne, Philip E and Brown, C Titus and Buck, Stuart and Kenall, Amye and Lin, Jennifer and McDougall, Damon and Nosek, Brian A and Ram, Karthik and   Soderberg, Courtney K and Spies, Jeffrey R and Thaney, Kaitlin and Updegrove, Andrew and Woo, Kara H and Yarkoni, Tal},
  editor = {Rodgers, Peter},
  volume = 5,
  year = 2016,
  month = {jul},
  pub_date = {2016-07-07},
  pages = {e16800},
  citation = {eLife 2016;5:e16800},
  doi = {10.7554/eLife.16800},
  url = {https://doi.org/10.7554/eLife.16800},
  keywords = {open access, open data, open science, open source, research},
  journal = {eLife},
  issn = {2050-084X},
  publisher = {eLife Sciences Publications, Ltd},
}

@article{piwowar_citation_2011,
	author = {Piwowar, Heather A. and Vision, Todd J. and Whitlock, Michael C.},
	date = {2011/05/01},
	date-added = {2022-10-26 13:49:38 -0400},
	date-modified = {2022-10-26 13:49:38 -0400},
	doi = {10.1038/473285a},
	id = {Piwowar2011},
	isbn = {1476-4687},
	journal = {Nature},
	number = {7347},
	pages = {285--285},
	title = {Data archiving is a good investment},
	url = {https://doi.org/10.1038/473285a},
	volume = {473},
	year = {2011},
	bdsk-url-1 = {https://doi.org/10.1038/473285a}}


@article{sansone_citation_2019,
	author = {Sansone, Susanna-Assunta and McQuilton, Peter and Rocca-Serra, Philippe and Gonzalez-Beltran, Alejandra and Izzo, Massimiliano and Lister, Allyson L. and Thurston, Milo and the FAIRsharing Community},
	date = {2019/04/01},
	date-added = {2023-02-01 10:22:01 -0500},
	date-modified = {2023-02-01 10:22:01 -0500},
	doi = {10.1038/s41587-019-0080-8},
	id = {Sansone2019},
	isbn = {1546-1696},
	journal = {Nature Biotechnology},
	number = {4},
	pages = {358--367},
	title = {FAIRsharing as a community approach to standards, repositories and policies},
	url = {https://doi.org/10.1038/s41587-019-0080-8},
	volume = {37},
	year = {2019},
	bdsk-url-1 = {https://doi.org/10.1038/s41587-019-0080-8}}


@article{tenopir_citation_2020,
    doi = {10.1371/journal.pone.0229003},
    author = {Tenopir, Carol AND Rice, Natalie M. AND Allard, Suzie AND Baird, Lynn AND Borycz, Josh AND Christian, Lisa AND Grant, Bruce AND Olendorf, Robert AND Sandusky, Robert J.},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    title = {Data sharing, management, use, and reuse: Practices and perceptions of scientists worldwide},
    year = {2020},
    month = {03},
    volume = {15},
    url = {https://doi.org/10.1371/journal.pone.0229003},
    pages = {1-26},
    number = {3},
}


@article{thessen_citation_2021,
	author = {Thessen, Anne E. AND Bogdan, Paul AND Patterson, David J. AND Casey, Theresa M. AND Hinojo-Hinojo, C{\'e}sar AND de Lange, Orlando AND Haendel, Melissa A.},
	doi = {10.1371/journal.pbio.3001129},
	journal = {PLOS Biology},
	month = {03},
	number = {3},
	pages = {1-12},
	publisher = {Public Library of Science},
	title = {From Reductionism to Reintegration: Solving society's most pressing problems requires building bridges between data types across the life sciences},
	url = {https://doi.org/10.1371/journal.pbio.3001129},
	volume = {19},
	year = {2021},
	bdsk-url-1 = {https://doi.org/10.1371/journal.pbio.3001129}
}

@article{vesteghem_citation_2020,
    author = {Vesteghem, Charles and Brøndum, Rasmus Froberg and Sønderkær, Mads and Sommer, Mia and Schmitz, Alexander and Bødker, Julie Støve and Dybkær, Karen and El-Galaly, Tarec Christoffer and Bøgsted, Martin},
    title = "{Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives}",
    journal = {Briefings in Bioinformatics},
    volume = {21},
    number = {3},
    pages = {936-945},
    year = {2020},
    month = {05},
    issn = {1477-4054},
    doi = {10.1093/bib/bbz044},
    url = {https://doi.org/10.1093/bib/bbz044},
    eprint = {https://academic.oup.com/bib/article-pdf/21/3/936/33398969/bbz044.pdf},
}

@article{wilkinson_citation_2016,
	author = {Wilkinson, Mark D. and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E. and Bouwman, Jildau and Brookes, Anthony J. and Clark, Tim and Crosas, Merc{\`e} and Dillo, Ingrid and Dumon, Olivier and Edmunds, Scott and Evelo, Chris T. and Finkers, Richard and Gonzalez-Beltran, Alejandra and Gray, Alasdair J. G. and Groth, Paul and Goble, Carole and Grethe, Jeffrey S. and Heringa, Jaap and 't Hoen, Peter A. C and Hooft, Rob and Kuhn, Tobias and Kok, Ruben and Kok, Joost and Lusher, Scott J. and Martone, Maryann E. and Mons, Albert and Packer, Abel L. and Persson, Bengt and Rocca-Serra, Philippe and Roos, Marco and van Schaik, Rene and Sansone, Susanna-Assunta and Schultes, Erik and Sengstag, Thierry and Slater, Ted and Strawn, George and Swertz, Morris A. and Thompson, Mark and van der Lei, Johan and van Mulligen, Erik and Velterop, Jan and Waagmeester, Andra and Wittenburg, Peter and Wolstencroft, Katherine and Zhao, Jun and Mons, Barend},
	date = {2016/03/15},
	date-added = {2022-10-26 14:14:12 -0400},
	date-modified = {2022-10-26 14:14:12 -0400},
	doi = {10.1038/sdata.2016.18},
	id = {Wilkinson2016},
	isbn = {2052-4463},
	journal = {Scientific Data},
	number = {1},
	pages = {160018},
	title = {The FAIR Guiding Principles for scientific data management and stewardship},
	url = {https://doi.org/10.1038/sdata.2016.18},
	volume = {3},
	year = {2016},
	bdsk-url-1 = {https://doi.org/10.1038/sdata.2016.18}
}

@article{liu_imaging_2017,
	title = {The {Current} {Role} of {Image} {Compression} {Standards} in {Medical} {Imaging}},
	volume = {8},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/2078-2489/8/4/131},
	doi = {10.3390/info8040131},
	abstract = {With the increasing utilization of medical imaging in clinical practice and the growing dimensions of data volumes generated by various medical imaging modalities, the distribution, storage, and management of digital medical image data sets requires data compression. Over the past few decades, several image compression standards have been proposed by international standardization organizations. This paper discusses the current status of these image compression standards in medical imaging applications together with some of the legal and regulatory issues surrounding the use of compression in medical settings.},
	language = {en},
	number = {4},
	urldate = {2022-01-10},
	journal = {Information},
	author = {Liu, Feng and Hernandez-Cabronero, Miguel and Sanchez, Victor and Marcellin, Michael W. and Bilgin, Ali},
	month = dec,
	year = {2017},
	note = {Number: 4
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {DICOM, HEVC, image compression, JPEG, JPEG-LS, JPEG-XR, JPEG2000, medical imaging, standards},
	pages = {131},
}


@misc{NIS,
	title = {{NIS} {Database} {Documentation}},
	url = {https://www.hcup-us.ahrq.gov/db/nation/nis/nisdbdocumentation.jsp},
	urldate = {2021-12-17},
}

@article{Afgan2018,
  doi = {10.1093/nar/gky379},
  url = {https://doi.org/10.1093/nar/gky379},
  year = {2018},
  month = may,
  publisher = {Oxford University Press ({OUP})},
  volume = {46},
  number = {W1},
  pages = {W537--W544},
  author = {Enis Afgan and Dannon Baker and B{\'{e}}r{\'{e}}nice Batut and Marius van~den~Beek and Dave Bouvier and Martin {\v{C}}ech and John Chilton and Dave Clements and Nate Coraor and Bj\"{o}rn A Gr\"{u}ning and Aysam Guerler and Jennifer Hillman-Jackson and Saskia Hiltemann and Vahid Jalili and Helena Rasche and Nicola Soranzo and Jeremy Goecks and James Taylor and Anton Nekrutenko and Daniel Blankenberg},
  title = {The Galaxy platform for accessible,  reproducible and collaborative biomedical analyses: 2018 update},
  journal = {Nucleic Acids Research}
}

@article{divio,
 url = {https://docs.divio.com/documentation-system/},
 title = {The Documentation System},
 author = {Divio team},
 year = {2024},
}

@blog{Alexakis2017,
    author = {Alex Alexakis},
    title = {You're not your user},
    url  = {https://blog.prototypr.io/dear-product-managers-youre-not-your-users-e5739627cbc8},
}

@website{Babich,
    author = {Nick Babich},
    year = {2019},
    title = {The 4 Golden Rules of UI Design},
    url  = {https://xd.adobe.com/ideas/process/ui-design/4-golden-rules-ui-design/},
}

@blog{Babich2017,
    author = {Nick Babich},
    title = {F-Shaped Pattern for Reading Content},
    url  = {https://uxplanet.org/f-shaped-pattern-for-reading-content-80af79cd3394},
}

@website{Bodner2018,
    author = {Herbet Bodner},
    year = {2018},
    title = {10 Reasons Why Code Reviews Make Better Code and Better Teams},
    url  = {https://simpleprogrammer.com/why-code-reviews-make-better-code-teams/},
}

@article{Bolchini2008,
  doi = {10.1093/bioinformatics/btn633},
  url = {https://doi.org/10.1093/bioinformatics/btn633},
  year = {2008},
  month = dec,
  publisher = {Oxford University Press ({OUP})},
  volume = {25},
  number = {3},
  pages = {406--412},
  author = {Davide Bolchini and Anthony Finkelstein and Vito Perrone and Sylvia Nagl},
  title = {Better bioinformatics through usability analysis},
  journal = {Bioinformatics}
}

@article{Budd2015,
  doi = {10.1371/journal.pcbi.1003972},
  url = {https://doi.org/10.1371/journal.pcbi.1003972},
  year = {2015},
  month = feb,
  publisher = {Public Library of Science ({PLoS})},
  volume = {11},
  number = {2},
  pages = {e1003972},
  author = {Aidan Budd and Manuel Corpas and Michelle D. Brazas and Jonathan C. Fuller and Jeremy Goecks and Nicola J. Mulder and Magali Michaut and B. F. Francis Ouellette and Aleksandra Pawlik and Niklas Blomberg},
  editor = {Amarda Shehu},
  title = {A Quick Guide for Building a Successful Bioinformatics Community},
  journal = {{PLOS} Computational Biology}
}

@website{Cronin2019,
    author = {Mike Cronin},
    year = {2019},
    title = {What Makes a Good Code Comment?},
    url  = {https://itnext.io/what-makes-a-good-code-comment-5267debd2c24},
}

@website{Csontos2019,
    author = {Anna-Zsófia Csontos},
    year = {2019},
    title = {All You Need to Know to Run Successful Usability Testing},
    url  = {https://uxstudioteam.com/ux-blog/usability-testing/},
}

@article{deMatos2013,
  doi = {10.1186/1471-2105-14-103},
  url = {https://doi.org/10.1186/1471-2105-14-103},
  year = {2013},
  publisher = {Springer Science and Business Media {LLC}},
  volume = {14},
  number = {1},
  pages = {103},
  author = {Paula de Matos and Jennifer A Cham and Hong Cao and Rafael Alc{\'{a}}ntara and Francis Rowland and Rodrigo Lopez and Christoph Steinbeck},
  title = {The Enzyme Portal: a case study in applying user-centered design methods in bioinformatics},
  journal = {{BMC} Bioinformatics}
}

@article{Duck2016,
  doi = {10.1371/journal.pone.0157989},
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  year = {2016},
  month = jun,
  publisher = {Public Library of Science ({PLoS})},
  volume = {11},
  number = {6},
  pages = {e0157989},
  author = {Geraint Duck and Goran Nenadic and Michele Filannino and Andy Brass and David L. Robertson and Robert Stevens},
  editor = {Shoba Ranganathan},
  title = {A Survey of Bioinformatics Database and Software Usage through Mining the Literature},
  journal = {{PLOS} {ONE}}
}

@article{Bolyen2019,
  doi = {10.1038/s41587-019-0209-9},
  url = {https://doi.org/10.1038/s41587-019-0209-9},
  year = {2019},
  month = jul,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {37},
  number = {8},
  pages = {852--857},
  author = {Evan Bolyen and Jai Ram Rideout and Matthew R. Dillon and Nicholas A. Bokulich and Christian C. Abnet and Gabriel A. Al-Ghalith and Harriet Alexander and Eric J. Alm and Manimozhiyan Arumugam and Francesco Asnicar and Yang Bai and Jordan E. Bisanz and Kyle Bittinger and Asker Brejnrod and Colin J. Brislawn and C. Titus Brown and Benjamin J. Callahan and Andr{\'{e}}s Mauricio Caraballo-Rodr{\'{\i}}guez and John Chase and Emily K. Cope and Ricardo Da Silva and Christian Diener and Pieter C. Dorrestein and Gavin M. Douglas and Daniel M. Durall and Claire Duvallet and Christian F. Edwardson and Madeleine Ernst and Mehrbod Estaki and Jennifer Fouquier and Julia M. Gauglitz and Sean M. Gibbons and Deanna L. Gibson and Antonio Gonzalez and Kestrel Gorlick and Jiarong Guo and Benjamin Hillmann and Susan Holmes and Hannes Holste and Curtis Huttenhower and Gavin A. Huttley and Stefan Janssen and Alan K. Jarmusch and Lingjing Jiang and Benjamin D. Kaehler and Kyo Bin Kang and Christopher R. Keefe and Paul Keim and Scott T. Kelley and Dan Knights and Irina Koester and Tomasz Kosciolek and Jorden Kreps and Morgan G. I. Langille and Joslynn Lee and Ruth Ley and Yong-Xin Liu and Erikka Loftfield and Catherine Lozupone and Massoud Maher and Clarisse Marotz and Bryan D. Martin and Daniel McDonald and Lauren J. McIver and Alexey V. Melnik and Jessica L. Metcalf and Sydney C. Morgan and Jamie T. Morton and Ahmad Turan Naimey and Jose A. Navas-Molina and Louis Felix Nothias and Stephanie B. Orchanian and Talima Pearson and Samuel L. Peoples and Daniel Petras and Mary Lai Preuss and Elmar Pruesse and Lasse Buur Rasmussen and Adam Rivers and Michael S. Robeson and Patrick Rosenthal and Nicola Segata and Michael Shaffer and Arron Shiffer and Rashmi Sinha and Se Jin Song and John R. Spear and Austin D. Swafford and Luke R. Thompson and Pedro J. Torres and Pauline Trinh and Anupriya Tripathi and Peter J. Turnbaugh and Sabah Ul-Hasan and Justin J. J. van der Hooft and Fernando Vargas and Yoshiki V{\'{a}}zquez-Baeza and Emily Vogtmann and Max von Hippel and William Walters and Yunhu Wan and Mingxun Wang and Jonathan Warren and Kyle C. Weber and Charles H. D. Williamson and Amy D. Willis and Zhenjiang Zech Xu and Jesse R. Zaneveld and Yilong Zhang and Qiyun Zhu and Rob Knight and J. Gregory Caporaso},
  title = {Reproducible,  interactive,  scalable and extensible microbiome data science using {QIIME} 2},
  journal = {Nature Biotechnology}
}

@article{deMatos2013,
  doi = {10.1186/1471-2105-14-103},
  url = {https://doi.org/10.1186/1471-2105-14-103},
  year = {2013},
  publisher = {Springer Science and Business Media {LLC}},
  volume = {14},
  number = {1},
  pages = {103},
  author = {Paula de Matos and Jennifer A Cham and Hong Cao and Rafael Alc{\'{a}}ntara and Francis Rowland and Rodrigo Lopez and Christoph Steinbeck},
  title = {The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics},
  journal = {{BMC} Bioinformatics}
}

@website{Frazee2014,
    author = {Alyssa Frazee},
    year = {2014},
    title = {Some internet wisdom on R documentation},
    url  = {http://alyssafrazee.com/2014/04/20/rdocs.html},
}

@website{Gitlab,
    author = {GitLab},
    title = {Writing a usability testing script},
    url  = {https://about.gitlab.com/handbook/engineering/ux/ux-research-training/writing-usability-testing-script/},
}

@website{Hotjar2020,
    author = {HotJar},
    year = {2019},
    title = {How to run moderated usability testing},
    url  = {https://www.hotjar.com/usability-testing/process-examples/},
}

@website{Herothemes,
    author = {Herothemes},
    year = {2020},
    title = {8 Best Knowledge Base Software Compared (Pros & Cons)},
    url  = {https://herothemes.com/blog/best-knowledge-base-software/},
}

@article{Javahery2004,
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  author = {Homa Javahery and Ahmed Seffah and Thiruvengadam Radhakrishnan},
  title = {Beyond power},
  journal = {Communications of the {ACM}}
}

@article{Karimzadeh2017,
  doi = {10.1093/bib/bbw134},
  url = {https://doi.org/10.1093/bib/bbw134},
  year = {2017},
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  publisher = {Oxford University Press ({OUP})},
  volume = {19},
  number = {4},
  pages = {693--699},
  author = {Mehran Karimzadeh and Michael M Hoffman},
  title = {Top considerations for creating bioinformatics software documentation},
  journal = {Briefings in Bioinformatics}
}

@website{Keeton2019,
    author = {B.J. Keeto},
    year = {2019},
    title = {How to Comment Your Code Like a Pro: Best Practices and Good Habits},
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}

@website{Krug2010,
    author = {Steve Krug},
    year = {2010},
    title = {Rocket Surgery Made Easy:The Do-It-Yourself Guide to Finding and Fixing Usability Problems},
    url  = {https://sensible.com/downloads/things-a-therapist-would-say.pdf},
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@article{Kumar2007,
  doi = {10.1093/bioinformatics/btm239},
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  year = {2007},
  month = may,
  publisher = {Oxford University Press ({OUP})},
  volume = {23},
  number = {14},
  pages = {1713--1717},
  author = {S. Kumar and J. Dudley},
  title = {Bioinformatics software for biologists in the genomics era},
  journal = {Bioinformatics}
}

@article{Love2014,
  doi = {10.1186/s13059-014-0550-8},
  url = {https://doi.org/10.1186/s13059-014-0550-8},
  year = {2014},
  month = dec,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {15},
  number = {12},
  author = {Michael I Love and Wolfgang Huber and Simon Anders},
  title = {Moderated estimation of fold change and dispersion for {RNA}-seq data with {DESeq}2},
  journal = {Genome Biology}
}

@article{Mangul2019,
  doi = {10.1186/s13059-019-1649-8},
  url = {https://doi.org/10.1186/s13059-019-1649-8},
  year = {2019},
  month = feb,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {20},
  number = {1},
  author = {Serghei Mangul and Lana S. Martin and Eleazar Eskin and Ran Blekhman},
  title = {Improving the usability and archival stability of bioinformatics software},
  journal = {Genome Biology}
}

@article{Mangul2019b,
  doi = {10.1371/journal.pbio.3000333},
  url = {https://doi.org/10.1371/journal.pbio.3000333},
  year = {2019},
  month = jun,
  publisher = {Public Library of Science ({PLoS})},
  volume = {17},
  number = {6},
  pages = {e3000333},
  author = {Serghei Mangul and Thiago Mosqueiro and Richard J. Abdill and Dat Duong and Keith Mitchell and Varuni Sarwal and Brian Hill and Jaqueline Brito and Russell Jared Littman and Benjamin Statz and Angela Ka-Mei Lam and Gargi Dayama and Laura Grieneisen and Lana S. Martin and Jonathan Flint and Eleazar Eskin and Ran Blekhman},
  title = {Challenges and recommendations to improve the installability and archival stability of omics computational tools},
  journal = {{PLOS} Biology}
}

@website{Meza2018,
    author = {Frank Meza},
    year = {2018},
    title = {The Value of Code Documentation},
    url  = {https://www.olioapps.com/blog/the-value-of-code-documentation/},
}

@Article{Molder2021,
  author = { Molder, F and Jablonski, KP and Letcher, B and Hall, MB and Tomkins-Tinch, CH and Sochat, V and Forster, J and Lee, S and Twardziok, SO and Kanitz, A and Wilm, A and Holtgrewe, M and Rahmann, S and Nahnsen, S and K�ster, J},
  title = {Sustainable data analysis with Snakemake [version 1; peer review: 1 approved, 1 approved with reservations]
},
  journal = {F1000Research},
  volume = {10},
  year = {2021},
  number = {33},
  doi = {10.12688/f1000research.29032.1}
}

@website{Moon2011,
    author = {Garrett Moon},
    year = {2011},
    title = {10 Tips For Creating a Killer FAQ Page},
    url  = {https://www.socialmediatoday.com/content/10-tips-creating-killer-faq-page},
}

@website{Moran2019,
    author = {Kate Moran},
    year = {2019},
    title = {Usability Testing 101},
    url  = {https://www.nngroup.com/articles/usability-testing-101/},
}

@article{Mulder2018,
  doi = {10.1371/journal.pcbi.1005772},
  url = {https://doi.org/10.1371/journal.pcbi.1005772},
  year = {2018},
  month = feb,
  publisher = {Public Library of Science ({PLoS})},
  volume = {14},
  number = {2},
  pages = {e1005772},
  author = {Nicola Mulder and Russell Schwartz and Michelle D. Brazas and Cath Brooksbank and Bruno Gaeta and Sarah L. Morgan and Mark A. Pauley and Anne Rosenwald and Gabriella Rustici and Michael Sierk and Tandy Warnow and Lonnie Welch},
  editor = {Olga G. Troyanskaya},
  title = {The development and application of bioinformatics core competencies to improve bioinformatics training and education},
  journal = {{PLOS} Computational Biology}
}

@website{Oles2021,
    author = {Andrzej Oleś, Wolfgang Huber and Martin Morgan},
    year = {2021},
    title = {Authoring R Markdown vignettes},
    url  = {https://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html},
}

@article{Pavelin2012,
  doi = {10.1371/journal.pcbi.1002554},
  url = {https://doi.org/10.1371/journal.pcbi.1002554},
  year = {2012},
  month = jul,
  publisher = {Public Library of Science ({PLoS})},
  volume = {8},
  number = {7},
  pages = {e1002554},
  author = {Katrina Pavelin and Jennifer A. Cham and Paula de Matos and Cath Brooksbank and Graham Cameron and Christoph Steinbeck},
  editor = {Philip E. Bourne},
  title = {Bioinformatics Meets User-Centred Design: A Perspective},
  journal = {{PLoS} Computational Biology}
}
@article{Patro2017,
  doi = {10.1038/nmeth.4197},
  url = {https://doi.org/10.1038/nmeth.4197},
  year = {2017},
  month = mar,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {14},
  number = {4},
  pages = {417--419},
  author = {Rob Patro and Geet Duggal and Michael I Love and Rafael A Irizarry and Carl Kingsford},
  title = {Salmon provides fast and bias-aware quantification of transcript expression},
  journal = {Nature Methods}
}

@website{Porter,
    author = {Joshua Porter},
    title = {Principles of User Interface Design},
    url  = {http://bokardo.com/principles-of-user-interface-design/},
}

@article{Quinlan2010,
  doi = {10.1093/bioinformatics/btq033},
  url = {https://doi.org/10.1093/bioinformatics/btq033},
  year = {2010},
  month = jan,
  publisher = {Oxford University Press ({OUP})},
  volume = {26},
  number = {6},
  pages = {841--842},
  author = {Aaron R. Quinlan and Ira M. Hall},
  title = {{BEDTools}: a flexible suite of utilities for comparing genomic features},
  journal = {Bioinformatics}
}

@website{Rehan2019,
    author = {Adnan Rehan},
    year = {2019},
    title = {Build Online Community and Forum with these 8 Best Software},
    url  = {https://geekflare.com/online-community-software/},
}

@Manual{RStudioTeam2020,
  title = {RStudio: Integrated Development Environment for R},
  author = {{RStudio Team}},
  organization = {RStudio, PBC.},
  address = {Boston, MA},
  year = {2020},
  url = {http://www.rstudio.com/},
}

@website{Simon2020,
    author = {Justin Simon},
    year = {2020},
    title = {The Ultimate Guide to Easily Make Instructional Videos},
    url  = {https://www.techsmith.com/blog/instructional-videos/},
}

@blog{Soegaard2020,
    author = {Mads Soegaard},
    title = {Visual Hierarchy: Organizing content to follow natural eye movement patterns},
    url  = {https://www.interaction-design.org/literature/article/visual-hierarchy-organizing-content-to-follow-natural-eye-movement-patterns},
}

@website{OutlookStudios2020,
    author = {Outlook Studios},
    year = {2020},
    title = {6 Tools to Find Broken Links on Your Website},
    url  = {https://www.outlookstudios.com/tools-to-find-broken-links-on-your-website/},
}

@blog{Spertus2021,
    author = {Ellen Spertus},
    title = {Best practices for writing code comments},
    url  = {https://stackoverflow.blog/2021/07/05/best-practices-for-writing-code-comments/},
}
@blog{Spielman,
    author = {Stephanie Spielman},
    title = {Introduction to R - CB2R Data Science Workshop, Summer 2020},
    url  = {https://github.com/sjspielman/cb2r-ds-summer2020/blob/71cb11277e7383292bf727841ab5fa4ed43cfcbe/resources/introduction_to_R.Rmd#L92},
}

@article {Subramanian2005,
	author = {Subramanian, Aravind and Tamayo, Pablo and Mootha, Vamsi K. and Mukherjee, Sayan and Ebert, Benjamin L. and Gillette, Michael A. and Paulovich, Amanda and Pomeroy, Scott L. and Golub, Todd R. and Lander, Eric S. and Mesirov, Jill P.},
	title = {Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles},
	volume = {102},
	number = {43},
	pages = {15545--15550},
	year = {2005},
	doi = {10.1073/pnas.0506580102},
	publisher = {National Academy of Sciences},
	abstract = {Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.},
	issn = {0027-8424},
	URL = {https://www.pnas.org/content/102/43/15545},
	eprint = {https://www.pnas.org/content/102/43/15545.full.pdf},
	journal = {Proceedings of the National Academy of Sciences}
}

@website{Tidwell,
    author = {Jeniger Tidwell},
    year = {2021},
    title = {Organizing the Page:Layout of Page Elements},
    url  = {https://www.oreilly.com/library/view/designing-interfaces/0596008031/ch04.html},
}

@website{Trounce2019,
    author = {David Trounce},
    year = {2019},
    title = {7 Great Tools For Creating Your Own Video Tutorials},
    url  = {https://helpdeskgeek.com/free-tools-review/7-great-tools-for-creating-your-own-video-tutorials/},
}

@website{Wilson2020,
    author = {Lee Wilson},
    year = {2020},
    title = {25 of the Best Examples of Effective FAQ Pages},
    url  = {https://www.searchenginejournal.com/best-faq-page-examples/267709/},
}

@website{Wolf2016,
    author = {Damian Wolf},
    year = {2016},
    title = {Why Developers Write Horrible Documentation and How to Solve It},
    url  = {https://dzone.com/articles/why-developers-write-horrible-documentation-and-ho},
}

@Book{xie2015,
  title = {Dynamic Documents with {R} and knitr},
  author = {Yihui Xie},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2015},
  edition = {2nd},
  note = {ISBN 978-1498716963},
  url = {http://yihui.name/knitr/},
}


@misc{Aaberge2021,
	title = {Stop {Using} {Magic} {Numbers} and {Variables} in {Your} {Code}},
	url = {https://betterprogramming.pub/stop-using-magic-numbers-and-variables-in-your-code-4e86f008b84c},
	abstract = {No one will understand your program. Not even you},
	language = {en},
	urldate = {2021-11-02},
	journal = {Medium},
	author = {Aaberge, Martin Andersson},
	month = January,
	year = {2021},
}

@article{Baker2009,
	title = {1,500 scientists lift the lid on reproducibility},
	volume = {533},
	copyright = {2016 Nature Publishing Group},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/533452a},
	doi = {10.1038/533452a},
	abstract = {Survey sheds light on the ‘crisis’ rocking research.},
	language = {en},
	number = {7604},
	urldate = {2021-10-06},
	journal = {Nature},
	author = {Baker, Monya},
	month = {May},
	year = {2016},
	pages = {452--454},
}

@article{Baker2016,
	title = {1,500 scientists lift the lid on reproducibility},
	volume = {533},
	copyright = {2016 Nature Publishing Group},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/533452a},
	doi = {10.1038/533452a},
	abstract = {Survey sheds light on the ‘crisis’ rocking research.},
	language = {en},
	number = {7604},
	urldate = {2021-10-06},
	journal = {Nature},
	author = {Baker, Monya},
	month = {May},
	year = {2016},
	pages = {452--454},
}

@article{BeaulieuJones2017,
  doi = {10.1038/nbt.3780},
  url = {https://doi.org/10.1038/nbt.3780},
  year = {2017},
  month = {Mar},
  publisher = {Springer Science and Business Media {LLC}},
  volume = {35},
  number = {4},
  pages = {342--346},
  author = {Brett K Beaulieu-Jones and Casey S Greene},
  title = {Reproducibility of computational workflows is automated using continuous analysis},
  journal = {Nature Biotechnology}
}

@article{Benureau2018,
	title = {Re-run, {Repeat}, {Reproduce}, {Reuse}, {Replicate}: {Transforming} {Code} into {Scientific} {Contributions}},
	volume = {11},
	issn = {1662-5196},
	shorttitle = {Re-run, {Repeat}, {Reproduce}, {Reuse}, {Replicate}},
	url = {https://www.frontiersin.org/article/10.3389/fninf.2017.00069},
	doi = {10.3389/fninf.2017.00069},
	abstract = {Scientific code is different from production software. Scientific code, by producing results that are then analyzed and interpreted, participates in the elaboration of scientific conclusions. This imposes specific constraints on the code that are often overlooked in practice. We articulate, with a small example, five characteristics that a scientific code in computational science should possess: re-runnable, repeatable, reproducible, reusable, and replicable. The code should be executable (re-runnable) and produce the same result more than once (repeatable); it should allow an investigator to reobtain the published results (reproducible) while being easy to use, understand and modify (reusable), and it should act as an available reference for any ambiguity in the algorithmic descriptions of the article (replicable).},
	urldate = {2021-10-06},
	journal = {Frontiers in Neuroinformatics},
	author = {Benureau, Fabien C. Y. and Rougier, Nicolas P.},
	year = {2018},
	pages = {69},
}

@misc{Bernardo2021,
	title = {Best {Practices} for {R} {Programming}},
	url = {https://towardsdatascience.com/best-practices-for-r-programming-ec0754010b5a},
	abstract = {Writing clean code is a great skill to have when you are working collaboratively— here are some tips for making your R code a bit cleaner},
	language = {en},
	urldate = {2021-11-02},
	journal = {Medium},
	author = {Bernardo, Ivo},
	month = August,
	year = {2021},
}

@misc{Biostars2021,
	title = {How Do You Manage Your Files & Directories For Your Projects?},
	url = {www.biostars.org/p/821/},
	urldate = {2021-10-12},
	year = {2010},
}

@article{Brito2020,
  doi = {10.1093/gigascience/giaa056},
  url = {https://doi.org/10.1093/gigascience/giaa056},
  year = {2020},
  month = June,
  publisher = {Oxford University Press ({OUP})},
  volume = {9},
  number = {6},
  author = {Jaqueline J Brito and Jun Li and Jason H Moore and Casey S Greene and Nicole A Nogoy and Lana X Garmire and Serghei Mangul},
  title = {Recommendations to enhance rigor and reproducibility in biomedical research},
  journal = {{GigaScience}}
}

@misc{Broman,
	title = {Tools for {Reproducible} {Research}},
	url = {https://kbroman.org/Tools4RR/},
	author = {Karl Broman},
	abstract = {A course on tools for reproducible research, UW-Madison},
	urldate = {2021-10-11},
	year = {2016},
}

@website{Bryan2017,
  author = {Jenny Bryan},
  year = {2017},
  month = {December},
  title = {Project-oriented workflow},
  url = {https://www.tidyverse.org/blog/2017/12/workflow-vs-script/},
  journal = {Tidyverse Blog},
}

@website{Bryan2021,
  author = {Jenny Bryan and Jim Hester},
  title = {Happy Git and GitHub for the useR},
  url = {https://happygitwithr.com/},
	year = {2021},
}

@book{Cannell2021,
	title = {9 {Coding} best practices {\textbar} {R} for {Epidemiology}},
	url = {https://brad-cannell.github.io/r4epi/},
	abstract = {This is the textbook for Brad Cannell’s Introduction to R Programming for Epidemiologic Research course.},
	urldate = {2021-11-02},
	author = {Cannell, Brad},
	year = {2021},
}

@book{Chacon2014,
  title={Pro git},
  author={Chacon, Scott and Straub, Ben},
  year={2014},
  publisher={Apress}
}

@misc{Chang2021,
	author = {Winston Chang},
	title = {Generating random numbers},
	url = {http://www.cookbook-r.com/Numbers/Generating_random_numbers/},
	urldate = {2021-11-02},
	year = {2021}
}

@misc{Cronin2019,
	title = {What {Makes} a {Good} {Code} {Comment}?},
	url = {https://itnext.io/what-makes-a-good-code-comment-5267debd2c24},
	abstract = {How comments can clarify things code can’t},
	language = {en},
	urldate = {2021-10-29},
	journal = {Medium},
	author = {Cronin, Mike},
	month = October,
	year = {2019},
}

@misc{Csendes2020,
	title = {15 common coding mistakes data scientist make in {Python} (and how to fix them)},
	url = {https://towardsdatascience.com/15-common-coding-mistakes-data-scientist-make-in-python-and-how-to-fix-them-7760467498af},
	abstract = {Data scientists are known for writing bad code. Start improving your code quality by not making these mistakes.},
	language = {en},
	urldate = {2021-11-02},
	journal = {Medium},
	author = {Csendes, Gerold},
	month = December,
	year = {2020},
}

@misc{DataCarpentry2019,
	title = {Introduction to the Command Line for Genomics},
	url = {https://bioinformatics-core-shared-training.github.io/shell-genomics/07-organization/index.html},
  chapter = {Project Organization},
	urldate = {2021-10-12},
	year = {2019},
}

@misc{DataCarpentry2021,
	title = {Project {Organization} and {Management} for {Genomics}},
	url = {https://datacarpentry.org/organization-genomics/},
	urldate = {2021-10-12},
	year = {2021},
}


@misc{DataCarpentry2021b,
	title = {Best {Practices} for {Writing} {R} {Code} – {Programming} with {R}},
	url = {https://swcarpentry.github.io/r-novice-inflammation/06-best-practices-R/},
	urldate = {2021-11-02},
	year = {2021},
}

@misc{Diederich2012,
	title = {Stop {Writing} {Classes}},
	url = {https://pyvideo.org/pycon-us-2012/stop-writing-classes.html},
	language = {en},
	urldate = {2021-10-29},
	journal = {PyVideo.org},
	author = {Diederich, Jack},
	year = {2012},
}

@misc{DRY,
	title = {How {To} {Keep} {Your} {Code} {Dry}},
	url = {http://www.drycode.io},
	abstract = {How to keep your code DRY},
	urldate = {2021-10-29},
	year = {2021},
}

@misc{DRY2013,
	title = {Don't {Repeat} {Yourself} - {Programmer} 97-things},
	url = {https://web.archive.org/web/20131204221336/http://programmer.97things.oreilly.com/wiki/index.php/Don't_Repeat_Yourself},
	urldate = {2021-10-29},
	month = December,
	year = {2013},
}

@misc{Dubel2021,
	title = {5 {Tips} for {Writing} {Clean} {R} {Code} - {Leave} {Your} {Code} {Reviewer} {Commentless}},
	author = {Marcin Dubel},
	url = {https://appsilon.com/write-clean-r-code/},
	abstract = {Writing readable and maintainable R code is no small task. Here are our top 5 tips for making your code reviewer commentless - from basic comments to best programming practices.},
	language = {en-GB},
	urldate = {2021-11-02},
	journal = {Appsilon {\textbar} End­ to­ End Data Science Solutions},
	month = {Mar},
	year = {2021},
}

@misc{Driscoll2021,
	title = {Jupyter {Notebook}: {An} {Introduction} – {Real} {Python}},
	shorttitle = {Jupyter {Notebook}},
	url = {https://realpython.com/jupyter-notebook-introduction/},
	abstract = {In this step-by-step Python tutorial, you learn how to get started with The Jupyter Notebook, an open source web application that you can use to create and share documents that contain live code, equations, visualizations, and text.},
	language = {en},
	urldate = {2021-11-16},
	author = {Mike, Driscoll},
	note = {publisher: Real Python},
	year = {2021},
}

@article{Essawy2020,
	title = {A taxonomy for reproducible and replicable research in environmental modelling},
	volume = {134},
	issn = {1364-8152},
	url = {https://www.sciencedirect.com/science/article/pii/S1364815219311612},
	doi = {10.1016/j.envsoft.2020.104753},
	language = {en},
	urldate = {2021-10-06},
	journal = {Environmental Modelling \& Software},
	author = {Essawy, Bakinam T. and Goodall, Jonathan L. and Voce, Daniel and Morsy, Mohamed M. and Sadler, Jeffrey M. and Choi, Young Don and Tarboton, David G. and Malik, Tanu},
	month = {December},
	year = {2020},
	keywords = {Reproducibility, Replicability, Containers, Docker, Singularity},
	pages = {104753},
}

@misc{Fangohr2021,
	title = {Jupyter for {Computational} {Science} and {Data} {Science}},
	url = {https://fangohr.github.io/blog/jupyter-for-computational-science-and-data-science.html},
	journal = {Computational Science and Data Science},
	author = {Fangohr, Hans},
	month = April,
	year = {2021},
}

@misc{Frazee2014,
  author = {Alyssa Frazee},
	title = {Some internet wisdom on {R} documentation},
	url = {http://alyssafrazee.com/2014/04/20/rdocs.html},
	abstract = {I spent a lot of last week documenting an R package. I’m still learning how to write good user-facing features (including documentation) in my software, so I...},
	urldate = {2021-10-29},
	year = {2014},
}

@misc{Frey2021,
	title = {How and why to share scientific code},
	url = {https://towardsdatascience.com/how-and-why-to-share-scientific-code-64fbd385a67},
	abstract = {A simple guide to reproducible research without becoming a software engineer},
	language = {en},
	urldate = {2021-10-06},
	journal = {Medium},
	author = {Nathan C. Frey},
	month = April,
	year = {2021},
}

@misc{Ganderson2016,
  author = {Alexander Ganderson},
	title = {Writing {Great} {Scientific} {Code}},
	url = {http://alexanderganderson.github.io/code/2016/10/12/coding_tips.html},
	abstract = {Introduction},
	urldate = {2021-11-02},
	year = {2016},
	month = {October},
}

@misc{Geeksforgeeks2018,
	author = {Geeks for Geeks},
	title = {f-strings in {Python}},
	url = {https://www.geeksforgeeks.org/formatted-string-literals-f-strings-python/},
	abstract = {A Computer Science portal for geeks. It contains well written, well thought and well explained computer science and programming articles, quizzes and practice/competitive programming/company interview Questions.},
	language = {en-us},
	urldate = {2021-11-02},
	journal = {GeeksforGeeks},
	month = April,
	year = {2018},
}

@misc{GenoFab2021,
	title = {Repeatability \& {Reproducibility}},
	url = {https://blog.genofab.com/repeatability-vs-reproducibility},
	abstract = {Repeatability vs Reproducibility – In science, reproducibility, not just repeatability, is key. Find out how to make research more reproducible.},
	language = {en},
	urldate = {2021-10-06},
	year = {2021},
}

@misc{Goldberg2016,
	author = {Zachary Goldberg},
	title = {The {Six} {Commandments} of {Good} {Code}: {Write} {Code} that {Stands} the {Test} of {Time}},
	shorttitle = {The {Six} {Commandments} of {Good} {Code}},
	url = {https://www.toptal.com/software/six-commandments-of-good-code},
	abstract = {How do you define good code? Is it 100\% test coverage, or is it backwards compatibility with decade-old hardware? We may not be able to reach an end to this debate yet, but good software always seems to conform to a few certain qualities of code.

In this article, Toptal Freelance Software Engineer Zachary Goldber...},
	language = {en},
	urldate = {2021-11-02},
	journal = {Toptal Engineering Blog},
	year = {2016},
}

@book{Good2021,
	title = {Chapter 5 {Reproducible} research \#1 {\textbar} {R} {Programming} for {Research}},
	url = {https://geanders.github.io/RProgrammingForResearch/reproducible-research-1.html},
	abstract = {This is a bookdown version of the course notes for R Programming for Research, Colorado State University, Fall 2016.},
	urldate = {2021-11-02},
	year = {2021},
	author = {Good, Rachel Severson, {and} Nicholas, Brooke Anderson},
}

@misc{GooglePython,
	title = {styleguide},
	url = {https://google.github.io/styleguide/pyguide.html},
	abstract = {Style guides for Google-originated open-source projects},
	language = {en-US},
	urldate = {2021-10-29},
	journal = {styleguide},
	year = {2021},
}

@misc{GoogleR,
	title = {Google’s {R} {Style} {Guide}},
	url = {https://google.github.io/styleguide/Rguide.html},
	abstract = {Style guides for Google-originated open-source projects},
	language = {en-US},
	urldate = {2021-10-29},
	journal = {styleguide},
	year = {2021},
}


@misc{Hauer2018,
	title = {Code {Review} {Guidelines} for {Humans}},
	url = {https://phauer.com/2018/code-review-guidelines/},
	abstract = {Guidelines describing the required mindset and phrasing techniques for effective and respectful code reviews},
	language = {en-US},
	urldate = {2021-11-02},
	journal = {Philipp Hauer's Blog},
	author = {Hauer, Philipp},
	month = July,
	year = {2018},
}

misc{Harvie2018,
	title = {Version {Control} — {Why} {Do} {We} {Need} {It}?},
	url = {https://medium.com/lanceharvieruntime/version-control-why-do-we-need-it-1681f4888cec},
	abstract = {Complex code development is impossible without a Version Control System (VCS). Version Control is used to track and control changes to…},
	language = {en},
	urldate = {2021-10-20},
	journal = {Medium},
	author = {Harvie, Lance},
	month = December,
	year = {2018},
}

@misc{Heil2020,
  title={Reproducible Programming for Biologists Who Code - Part 1: Must Dos},
	url={https://autobencoder.com/2020-06-16-mustdo/}, journal={AutoBenCoding},
	author={Heil, Benjamin J.},
	year={2020},
	month={June},
}

@misc{Heil2020b,
  title = {Reproducible Programming for Biologists Who Code - Part 2: Should Dos},
  url = {https://autobencoder.com/2020-06-30-shoulddo/},
  journal = {AutoBenCoding},
	author = {Heil, Benjamin J.},
	year = {2020},
	month = {June},
}

@misc{Heroux2018,
	title = {Don’t repeat yourself: {Python} functions},
	shorttitle = {Don’t repeat yourself},
	url = {https://scientificallysound.org/2018/07/19/python-functions/},
	abstract = {Learning to program is not easy. We have to learn a new language and a new way of thinking. We have to learn the grammatical rules of the programming language we are learning, and the logic of our …},
	language = {en},
	urldate = {2021-11-29},
	journal = {Scientifically Sound},
	author = {Martin Héroux},
	month = July,
	year = {2018},
}

@misc{Hildebr2020,
	title = {Your {Code} {Sucks}! – {Code} {Review} {Best} {Practices}},
	url = {https://quickbirdstudios.com/blog/code-review-best-practices-guidelines/},
	abstract = {Plenty of things can go wrong in code reviews that can render the entire process useless. We waste time, money, energy and patience without really improving the quality of our code. There are tons of online courses and tutorials available writing code – but almost none for reviewing code. We intend to change that: Here's your ultimate guide for how to get the most of code reviews!},
	language = {en-US},
	urldate = {2021-11-02},
	journal = {QuickBird Studios Blog},
	author = {Hildebr, Mischa},
	month = mar,
	year = {2020},
}

@misc{Hobert2018,
	title = {Writing {Variable} — {Informative}, {Descriptive} \& {Elegant}},
	url = {https://medium.datadriveninvestor.com/writing-variable-informative-descriptive-elegant-1dd6f3f15db3},
	abstract = {There are only two hard things in Computer Science: cache invalidation and naming things. — Phil Karlton},
	language = {en},
	urldate = {2021-10-29},
	journal = {Medium},
	author = {Hobert, Kevin},
	month = September,
	year = {2018},
}

@article{Hothorn2011,
	title = {Case studies in reproducibility},
	volume = {12},
	issn = {1467-5463},
	url = {https://doi.org/10.1093/bib/bbq084},
	doi = {10.1093/bib/bbq084},
	abstract = {Reproducible research is a concept of providing access to data and software along with published scientific findings. By means of some case studies from different disciplines, we will illustrate reasons why readers should be given the possibility to look at the data and software independently from the authors of the original publication. We report results of a survey comprising 100 papers recently published in Bioinformatics. The main finding is that authors of this journal share a culture of making data available. However, the number of papers where source code for simulation studies or analyzes is available is still rather limited.},
	number = {3},
	urldate = {2021-10-06},
	journal = {Briefings in Bioinformatics},
	author = {Hothorn, Torsten and Leisch, Friedrich},
	month = May,
	year = {2011},
	pages = {288--300},
}

@article{Ioannidis2009,
	title = {Repeatability of published microarray gene expression analyses},
	volume = {41},
	issn = {1546-1718},
	doi = {10.1038/ng.295},
	abstract = {Given the complexity of microarray-based gene expression studies, guidelines encourage transparent design and public data availability. Several journals require public data deposition and several public databases exist. However, not all data are publicly available, and even when available, it is unknown whether the published results are reproducible by independent scientists. Here we evaluated the replication of data analyses in 18 articles on microarray-based gene expression profiling published in Nature Genetics in 2005-2006. One table or figure from each article was independently evaluated by two teams of analysts. We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced. The main reason for failure to reproduce was data unavailability, and discrepancies were mostly due to incomplete data annotation or specification of data processing and analysis. Repeatability of published microarray studies is apparently limited. More strict publication rules enforcing public data availability and explicit description of data processing and analysis should be considered.},
	language = {eng},
	number = {2},
	journal = {Nature Genetics},
	author = {Ioannidis, John P. A. and Allison, David B. and Ball, Catherine A. and Coulibaly, Issa and Cui, Xiangqin and Culhane, Aedín C. and Falchi, Mario and Furlanello, Cesare and Game, Laurence and Jurman, Giuseppe and Mangion, Jon and Mehta, Tapan and Nitzberg, Michael and Page, Grier P. and Petretto, Enrico and van Noort, Vera},
	month = February,
	year = {2009},
	pmid = {19174838},
	keywords = {Animals, Data Interpretation, Statistical, Databases, Genetic, Gene Expression Profiling, Genome-Wide Association Study, Humans, Oligonucleotide Array Sequence Analysis, Peer Review, Research, Publications, Reproducibility of Results},
	pages = {149--155},
}

@misc{Joseph2017,
	author = {Max Joseph, Leah Wasser, Software Carpentry, Reproducible Science Curriculum Community, Bryce Mecum},
	title = {Write {Efficient} {Scientific} {Code} - the {DRY} ({Don}’t {Repeat} {Yourself}) {Principle}},
	url = {https://www.earthdatascience.org/courses/earth-analytics/automate-science-workflows/write-efficient-code-for-science-r/},
	abstract = {This lesson will cover the basic principles of using functions and why they are important.},
	language = {en},
	urldate = {2021-11-29},
	journal = {Earth Data Science - Earth Lab},
	month = mar,
	year = {2017},
}

@inproceedings{Jupyter2016,
  booktitle = {Positioning and Power in Academic Publishing: Players, Agents and Agendas},
  editor = {Fernando Loizides and Birgit Scmidt},
  title = {Jupyter Notebooks - a publishing format for reproducible computational workflows},
  author = {Thomas Kluyver and Benjamin Ragan-Kelley and Fernando P{\'e}rez and Brian Granger and Matthias Bussonnier and Jonathan Frederic and Kyle Kelley and Jessica Hamrick and Jason Grout and Sylvain Corlay and Paul Ivanov and Dami{\'a}n Avila and Safia Abdalla and Carol Willing and  Jupyter development team},
  publisher = {IOS Press},
  address = {Netherlands},
  year = {2016},
  pages = {87--90},
  url = {https://eprints.soton.ac.uk/403913/},
  abstract = {It is increasingly necessary for researchers in all fields to write computer code, and in order to reproduce research results, it is important that this code is published. We present Jupyter notebooks, a document format for publishing code, results and explanations in a form that is both readable and executable. We discuss various tools and use cases for notebook documents.}
}

@misc{Keeton2019,
  author = {BJ Keeton},
  month = {April},
  year = {2019},
	title = {How to {Comment} {Your} {Code} {Like} a {Pro}: {Best} {Practices} and {Good} {Habits}},
	url = {https://www.elegantthemes.com/blog/wordpress/how-to-comment-your-code-like-a-pro-best-practices-and-good-habits},
	abstract = {Writing code is a lot like writing prose. Every person does it a little differently, and because of that, we all have a distinct voice when our code is read. We have different naming conventions and different problem-solving logic. We all think our code makes sense — especially if it works — but...},
	language = {en},
	urldate = {2021-10-29},
	journal = {Elegant Themes},
}

@misc{Klinefelter2016,
  author = {Sarah Klinefelter},
  month = {August},
  year = {2016},
	title = {{DRY} {Programming} {Practices} – {Metova}},
	url = {https://metova.com/dry-programming-practices/},
	language = {en-US},
	urldate = {2021-10-29},
}

@misc{Kostyuk2020,
	title = {Data {Science} {Python} {Best} {Practices}},
	url = {https://medium.com/bcggamma/data-science-python-best-practices-fdb16fdedf82},
	abstract = {Write production-level code!},
	language = {en},
	urldate = {2021-11-02},
	journal = {BCG GAMMA},
	author = {Kostyuk, Victor},
	month = May,
	year = {2020},
}

@misc{Koehrsen2019,
	title = {Data {Scientists}: {Your} {Variable} {Names} {Are} {Awful}. {Here}’s {How} to {Fix} {Them}.},
	shorttitle = {Data {Scientists}},
	url = {https://towardsdatascience.com/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them-89053d2855be},
	abstract = {A Simple Way to Greatly Improve Code Quality},
	language = {en},
	urldate = {2021-10-29},
	journal = {Medium},
	author = {Koehrsen, Will},
	month = July,
	year = {2019},
}

@misc{Lee2019,
	title = {Why {Git} {And} {How} {To} {Use} {Git} {As} {A} {Data} {Scientist}},
	url = {https://towardsdatascience.com/why-git-and-how-to-use-git-as-a-data-scientist-4fa2d3bdc197},
	abstract = {Perhaps you’ve heard of Git somewhere else.},
	language = {en},
	urldate = {2021-10-20},
	journal = {Medium},
	author = {Lee, Admond},
	month = December,
	year = {2019},
}

@misc{Meza2018,
	title = {The {Value} of {Code} {Documentation}},
	url = {https://www.olioapps.com/blog/the-value-of-code-documentation/},
	abstract = {Code documentation is the collection of easy to understand images and written descriptions that explain what a codebase does and how it can be used.},
	language = {en},
	urldate = {2021-10-29},
	journal = {Olio Apps},
	author = {Meza, Frank},
	month = February,
	year = {2018},
}

@misc{Mustafeez2021,
	author = {Anusheh Zohair Mustafeez},
	title = {Absolute vs. relative path},
	url = {https://www.educative.io/edpresso/absolute-vs-relative-path},
	language = {en-us},
	urldate = {2021-11-02},
	journal = {Educative},
	year = {2021},
}

@misc{Navarro2021,
	title = {Project structure},
	url = {https://www.youtube.com/playlist?list=PLRPB0ZzEYegPiBteC2dRn95TX9YefYFyy},
	language = {english},
	urldate = {2021-11-30},
	author = {Danielle Navarro},
	month = March,
	year = {2021},
}

@misc{Neuzerling2018,
	title = {{useR}: {Getting} started with {R} and {Docker}},
	shorttitle = {{useR}},
	url = {https://mdneuzerling.com/post/user-getting-started-with-r-and-docker/},
	abstract = {These are my notes for the super helpful tutorial given by Elizabeth Stark on the first day of the UseR 2018 conference. This was an introduction to Docker for R users who have no prior experience with Docker (which was me!).
 Elizabeth’s slides Elizabeth’s exercises and examples  This tutorial took me through setting up an RStudio Server container. I’m on a Linux machine, but I’m particularly interested by the idea that you could run these traditionally Linux-only servers on a Windows machine through Docker.},
	language = {en},
	urldate = {2021-11-17},
	month = July,
	year = {2018},
	author = {David Neuzerling},
}

@article{Orosz2019,
  url = {https://blog.pragmaticengineer.com/readable-code/},
  year = {2019},
  month = December,
  author = {Gergely Orosz},
  title = {Readable Code},
}

@misc{Okada2021,
	title = {How to {Run} {Jupyter} {Notebook} on {Docker}},
	url = {https://towardsdatascience.com/how-to-run-jupyter-notebook-on-docker-7c9748ed209f},
	abstract = {No more Python env and package update},
	language = {en},
	urldate = {2021-11-17},
	journal = {Medium},
	author = {Okada, Shinichi},
	month = August,
	year = {2021},
}

@misc{openscilabs2021,
	title = {Launching {RStudio} in {Docker}},
	url = {https://jsta.github.io/r-docker-tutorial/02-Launching-Docker.html},
	urldate = {2021-11-17},
	author = {openscilabs},
	year = {2021},
}

@article{Parker2017,
  doi = {10.7287/peerj.preprints.3210v1},
  url = {https://doi.org/10.7287/peerj.preprints.3210v1},
  year = {2017},
  month = August,
  publisher = {{PeerJ}},
  author = {Hilary Parker},
  title = {Opinionated analysis development}
}

@techreport{Patil2016,
	title = {A statistical definition for reproducibility and replicability},
	copyright = {© 2016, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/},
	url = {https://www.biorxiv.org/content/10.1101/066803v1},
	abstract = {Everyone agrees that reproducibility and replicability are fundamental characteristics of scientific studies. These topics are attracting increasing attention, scrutiny, and debate both in the popular press and the scientific literature. But there are no formal statistical definitions for these concepts, which leads to confusion since the same words are used for different concepts by different people in different fields. We provide formal and informal definitions of scientific studies, reproducibility, and replicability that can be used to clarify discussions around these concepts in the scientific and popular press.},
	language = {en},
	urldate = {2021-10-06},
	author = {Patil, Prasad and Peng, Roger D. and Leek, Jeffrey T.},
	month = July,
	year = {2016},
	note = {Type: article},
	pages = {066803},
}

@misc{PEP8,
	title = {{PEP} 8 -- {Style} {Guide} for {Python} {Code}},
	url = {https://www.python.org/dev/peps/pep-0008/},
	abstract = {The official home of the Python Programming Language},
	language = {en},
	urldate = {2021-10-29},
	journal = {Python.org},
	year = {2021},
}

@misc{Python2021,
	title = {Python 3's f-{Strings}: {An} {Improved} {String} {Formatting} {Syntax} ({Guide}) – {Real} {Python}},
	shorttitle = {Python 3's f-{Strings}},
	url = {https://realpython.com/python-f-strings/},
	abstract = {As of Python 3.6, f-strings are a great new way to format strings. Not only are they more readable, more concise, and less prone to error than other ways of formatting, but they are also faster! By the end of this article, you will learn how and why to start using f-strings today.},
	language = {en},
	urldate = {2021-11-02},
	author = {Real Python},
	year = {2021},
}

@misc{Programcreek2021,
	title = {Python {Examples} of pathlib.{Path}.joinpath},
	url = {https://www.programcreek.com/python/example/114070/pathlib.Path.joinpath},
	abstract = {This page shows Python examples of pathlib.Path.joinpath},
	urldate = {2021-11-02},
	year = {2021},
}

@misc{ProjectJupyter2018,
	title = {Jupyter {Docker} {Stacks} — docker-stacks latest documentation},
	url = {https://jupyter-docker-stacks.readthedocs.io/en/latest/index.html},
	urldate = {2021-11-17},
	year = {2018},
	name = {{Project Jupyter}},
}

@misc{Radigan2021,
	title = {Why code reviews matter (and actually save time!)},
	url = {https://www.atlassian.com/agile/software-development/code-reviews},
	abstract = {Code review helps developers learn the code base, as well as help them learn new technologies and techniques that grow their skill sets.},
	language = {en},
	urldate = {2021-11-02},
	journal = {Atlassian},
	author = {Dan Radigan},
	year = {2021},
}

@website{refinebio,
  author = {Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler.},
  title = {refine.bio: a resource of uniformly processed publicly available gene expression datasets.},
  url = {https://www.refine.bio},
	year = {2021},
}

@misc{Riffomonas2021,
	author = {{Riffomonas Project}},
	title = {Keeping {R} code {DRY} with functions: {Don}'t repeat yourself! ({CC096})},
	shorttitle = {Keeping {R} code {DRY} with functions},
	url = {https://www.youtube.com/watch?v=XSRO4VKD-pc},
	abstract = {Don't repeat yourself or the DRY principle is one of the best practices to writing good R. When you repeat the same block of code you risk introducing errors...},
	language = {en},
	urldate = {2021-11-29},
	year = {2021},
	month = {November},
}

@Manual{rmarkdown2021,
  title = {rmarkdown: Dynamic Documents for R},
  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
  year = {2021},
  note = {R package version 2.10},
  url = {https://github.com/rstudio/rmarkdown},
}

@article{Sandve2013,
	title = {Ten {Simple} {Rules} for {Reproducible} {Computational} {Research}},
	volume = {9},
	issn = {1553-7358},
	url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285},
	doi = {10.1371/journal.pcbi.1003285},
	language = {en},
	number = {10},
	urldate = {2021-10-06},
	journal = {PLOS Computational Biology},
	author = {Sandve, Geir Kjetil and Nekrutenko, Anton and Taylor, James and Hovig, Eivind},
	month = October,
	year = {2013},
	keywords = {Computer applications, Reproducibility, Archives, Computer and information sciences, Source code, Genome analysis, Habits, Replication studies},
	pages = {e1003285},
}

@misc{SoftwareCarpentry2021,
	title = {Version {Control} with {Git}},
	url = {https://swcarpentry.github.io/git-novice/},
	urldate = {2021-10-06},
	year = {2021},
}

@book{Savonen2021,
  author = {Candace Savonen},
	title = {Chapter 8 {Creating} clarifying code comments {\textbar} {Documentation} and {Usability}},
	url = {https://jhudatascience.org/Documentation_and_Usability/creating-clarifying-code-comments.html#creating-clarifying-code-comments},
	abstract = {A course to cover the basics of creating documentation and tutorials to maximize the usability of ITCR tools.},
	urldate = {2021-10-29},
	year = {2021},
}

@misc{Savonen2021b,
	author = {Candace Savonen},
	title = {The {Childhood} {Cancer} {Data} {Lab}'s not-so-secret sauce for efficient workflows — aka {Philadelphia}’s third most famous process},
	url = {https://www.ccdatalab.org/blog/2021/10/7/not-so-secret-sauce-for-efficient-workflows},
	abstract = {‘Work smarter not harder’ is useless advice if you don’t know  how  to ‘work smarter’. But the Childhood Cancer Data Lab's work and processes may be the smartest I’ve ever had the pleasure of learning and adopting. Their processes are just as valuable to me now that I’ve moved on to the next stage o},
	language = {en-US},
	urldate = {2021-11-02},
	journal = {Childhood Cancer Data Lab},
	month = {October},
	year = {2021},
}

@misc{Saxena2021,
	title = {6 {Mistakes} {Every} {Python} {Beginner} {Should} {Avoid} {While} {Coding}},
	url = {https://towardsdatascience.com/6-mistakes-every-python-beginner-should-avoid-while-coding-e57e14917942},
	abstract = {These small improvements can be crucial},
	language = {en},
	urldate = {2021-11-02},
	journal = {Medium},
	author = {Saxena, Pranjal},
	month = August,
	year = {2021},
}

@misc{Spertus2021,
	title = {Best practices for writing code comments},
	url = {https://stackoverflow.blog/2021/07/05/best-practices-for-writing-code-comments/},
	abstract = {While there are many resources to help programmers write better code—such as books and static analyzers—there are few for writing better comments. While it's easy to measure the quantity of comments in a program, it's hard to measure the quality, and the two are not necessarily correlated. A bad comment is worse than no comment at all. Here are some rules to help you achieve a happy medium.},
	language = {en-US},
	urldate = {2021-10-29},
	journal = {Stack Overflow Blog},
	author = {Spertus, Ellen},
	month = July,
	year = {2021},
}

@software{Shapiro2021,
  author = {Shapiro, Joshua A. and Savonen, Candace L. and Hawkins, Allegra G. and Bethell, Chante J. and Venkatesh Prasad, Deepashree and Greene, Casey S. and Taroni, Jaclyn N.},
  month = {June},
  title = {{Childhood Cancer Data Lab Training Modules}},
  version = {2021-june},
  year = {2021}
  }

@misc{Severin2021,
	title = {Project {Management}},
	url = {https://bioinformaticsworkbook.org/projectManagement/Intro_projectManagement.html},
	abstract = {A workbook to help scientists working on bioinformatics projects},
	language = {en},
	urldate = {2021-10-14},
	journal = {Bioinformatics Workbook},
	author = {Severin, Andrew},
	year = {2021},
}

@article{Shih2017,
  doi = {10.1158/2159-8290.cd-16-1049},
  url = {https://doi.org/10.1158/2159-8290.cd-16-1049},
  year = {2017},
  month = February,
  publisher = {American Association for Cancer Research ({AACR})},
  volume = {7},
  number = {5},
  pages = {494--505},
  author = {Alan H. Shih and Cem Meydan and Kaitlyn Shank and Francine E. Garrett-Bakelman and Patrick S. Ward and Andrew M. Intlekofer and Abbas Nazir and Eytan M. Stein and Kristina Knapp and Jacob Glass and Jeremy Travins and Kim Straley and Camelia Gliser and Christopher E. Mason and Katharine Yen and Craig B. Thompson and Ari Melnick and Ross L. Levine},
  title = {Combination Targeted Therapy to Disrupt Aberrant Oncogenic Signaling and Reverse Epigenetic Dysfunction in {IDH}2- and {TET}2-Mutant Acute Myeloid Leukemia},
  journal = {Cancer Discovery}
}

@misc{Smartbear2021,
	title = {Best {Practices} for {Code} {Review}},
	url = {https://smartbear.com/en/learn/code-review/best-practices-for-peer-code-review/},
	abstract = {A successful peer review strategy requires balance between strictly documented processes and a non-threatening, collaborative environment. Highly regimented peer reviews can stifle productivity, yet lackadaisical processes are often ineffective. Managers are responsible for finding a middle groun...},
	urldate = {2021-11-02},
	journal = {smartbear.com},
	year = {2021},
	author = {Smartbear Team},
}

@misc{Smith2013,
	author = {Steve Smith},
	title = {Don't {Repeat} {Yourself} - {Programmer} 97-things},
	url = {https://web.archive.org/web/20131204221336/http://programmer.97things.oreilly.com/wiki/index.php/Don't_Repeat_Yourself},
	urldate = {2021-11-02},
	month = December,
	year = {2013},
}

@misc{Soage2020,
	author = {Jose Carlos Soage},
	title = {{SET} {SEED} in {R} with set.seed() function ▷ [{WITH} {EXAMPLES}]},
	url = {https://r-coder.com/set-seed-r/},
	abstract = {Set seed in R to generate reproducible pseudorandom numbers 🌱🌱 Learn the meaning of setseed in R, why to use the set.seed function and how it works},
	language = {en-US},
	urldate = {2021-11-02},
	journal = {R CODER},
	month = July,
	year = {2020},
}

@blog{Spielman,
    author = {Stephanie Spielman},
    title = {Introduction to R - CB2R Data Science Workshop, Summer 2020},
    url  = {https://github.com/sjspielman/cb2r-ds-summer2020/blob/71cb11277e7383292bf727841ab5fa4ed43cfcbe/resources/introduction_to_R.Rmd#L92},
}

@misc{Srivastav2018,
	title = {A {Docker} {Tutorial} for {Beginners}},
	url = {https://docker-curriculum.com/},
	abstract = {Learn to build and deploy your distributed applications easily to the cloud with Docker},
	language = {en-us},
	urldate = {2021-11-17},
	journal = {A Docker Tutorial for Beginners},
	author = {Srivastav, Prakhar},
	year = {2018},
}

@misc{Tayo2019,
	title = {How to {Organize} {Your} {Data} {Science} {Project}},
	url = {https://towardsdatascience.com/how-to-organize-your-data-science-project-dd6599cf000a},
	abstract = {A tutorial on data science project organization},
	language = {en},
	urldate = {2021-10-12},
	journal = {Medium},
	author = {Benjamin Obi Tayo},
	month = December,
	year = {2019},
}

@misc{Tidyverse2021,
	title = {Read a delimited file (including {CSV} and {TSV}) into a tibble — read\_delim},
	url = {https://readr.tidyverse.org/reference/read_delim.html},
	abstract = {read\_csv() and read\_tsv() are special cases of the more general
read\_delim(). They're useful for reading the most common types of
flat file data, comma separated values and tab separated values,
respectively. read\_csv2() uses ; for the field separator and , for the
decimal point. This format is common in some European countries.},
	language = {en},
	urldate = {2021-11-02},
}

@misc{Tran2021,
	title = {Python {Clean} {Code}: 6 {Best} {Practices} to {Make} your {Python} {Functions} more {Readable}},
	shorttitle = {Python {Clean} {Code}},
	url = {https://towardsdatascience.com/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60},
	abstract = {Stop Writing Python Functions that Take more than 3 Minutes to Understand},
	language = {en},
	urldate = {2021-11-05},
	journal = {Medium},
	author = {Tran, Khuyen},
	month = January,
	year = {2021},
}

@misc{Vidhya2019,
	author = {Analytics Vidhya Team},
	title = {What is {Tidyverse} {\textbar} {Tidyverse} {Package} in {R}},
	url = {https://www.analyticsvidhya.com/blog/2019/05/beginner-guide-tidyverse-most-powerful-collection-r-packages-data-science/},
	abstract = {Tidyverse is the most powerful collection of R packages. Learn about the tidyverse package in R and how each package works and get the full code here.},
	language = {en},
	urldate = {2021-11-02},
	journal = {Analytics Vidhya},
	month = May,
	year = {2019},
}

@misc{Vickery2021,
	title = {4 {Tools} for {Reproducible} {Jupyter} {Notebooks}},
	url = {https://towardsdatascience.com/4-tools-for-reproducible-jupyter-notebooks-d7423721bd04},
	abstract = {Jupyter notebooks have a somewhat poor reputation in the wider programming community. Joel Grus’ famous “I don’t like notebooks” talk, which he bravely gave at JupyterCon in 2018, covered many of the…},
	language = {en},
	urldate = {2021-10-06},
	journal = {Medium},
	author = {Vickery, Rebecca},
	month = May,
	year = {2021},
}

@misc{Wasser2019,
	author = {Leah Wasser, Jenny Palomino},
	title = {{DRY} {Code} and {Modularity}},
	url = {https://www.earthdatascience.org/courses/intro-to-earth-data-science/write-efficient-python-code/intro-to-clean-code/dry-modular-code/},
	abstract = {DRY (Do Not Repeat Yourself) code supports reproducibility by removing repetition and making code easier to read. Learn about key strategies to write DRY code in Python.},
	language = {en},
	urldate = {2021-11-29},
	journal = {Earth Data Science - Earth Lab},
	month = September,
	year = {2019},
}

@misc{Wickham,
  author = {Hadley Wickham},
	title = {Style guide · {Advanced} {R}.},
	url = {http://adv-r.had.co.nz/Style.html},
	urldate = {2021-10-29},
	year = {2019},
}

@book{Wright2021,
	title = {Chapter 1 {Introduction} to the {Tidyverse} {\textbar} {Tidyverse} {Skills} for {Data} {Science}},
	url = {http://jhudatascience.org/tidyversecourse/intro.html},
	abstract = {This book demonstrates how to use the Tidyverse collection of packages for doing data science.},
	urldate = {2021-11-02},
	author = {Carrie Wright, Shannon E. Ellis, Stephanie C. Hicks {and} Roger D. Peng},
}

@Book{Xie2018,
  title = {R Markdown: The Definitive Guide},
  author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2018},
  note = {ISBN 9781138359338},
  url = {https://bookdown.org/yihui/rmarkdown},
}

@Book{Xie2020,
  title = {R Markdown Cookbook},
  author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
  publisher = {Chapman and Hall/CRC},
  address = {Boca Raton, Florida},
  year = {2020},
  note = {ISBN 9780367563837},
  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
}

@misc{Zheng2018,
	title = {A {Quick} {Primer} to {Version} {Control} {Using} {Git}},
	url = {https://towardsdatascience.com/a-quick-primer-to-version-control-using-git-3fbdbb123262},
	abstract = {Version control is a type of system that allows you to keep track of changes made to your code over time. As such, version control is…},
	language = {en},
	urldate = {2021-10-20},
	journal = {Medium},
	author = {Zheng, Paulina},
	month = September,
	year = {2018},
}


@article{samuel_understanding_2021,
	title = {Understanding experiments and research practices for reproducibility: an exploratory study},
	volume = {9},
	copyright = {https://creativecommons.org/licenses/by/4.0/},
	issn = {2167-8359},
	shorttitle = {Understanding experiments and research practices for reproducibility},
	url = {https://peerj.com/articles/11140},
	doi = {10.7717/peerj.11140},
	abstract = {Scientific experiments and research practices vary across disciplines. The research practices followed by scientists in each domain play an essential role in the understandability and reproducibility of results. The ‘‘Reproducibility Crisis’’, where researchers find difficulty in reproducing published results, is currently faced by several disciplines. To understand the underlying problem in the context of the reproducibility crisis, it is important to first know the different research practices followed in their domain and the factors that hinder reproducibility. We performed an exploratory study by conducting a survey addressed to researchers representing a range of disciplines to understand scientific experiments and research practices for reproducibility. The survey findings identify a reproducibility crisis and a strong need for sharing data, code, methods, steps, and negative and positive results. Insufficient metadata, lack of publicly available data, and incomplete information in study methods are considered to be the main reasons for poor reproducibility. The survey results also address a wide number of research questions on the reproducibility of scientific results. Based on the results of our explorative study and supported by the existing published literature, we offer general recommendations that could help the scientific community to understand, reproduce, and reuse experimental data and results in the research data lifecycle.},
	language = {en},
	urldate = {2025-11-26},
	journal = {PeerJ},
	author = {Samuel, Sheeba and König-Ries, Birgitta},
	month = apr,
	year = {2021},
	pages = {e11140},
}