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@article{altschul2013anatomy,
Author = {Altschul, Stephen and Demchak, Barry and Durbin, Richard and Gentleman, Robert and Krzywinski, Martin and Li, Heng and Nekrutenko, Anton and Robinson, James and Rasband, Wayne and Taylor, James and others},
Date-Added = {2017-09-07 16:17:44 +0000},
Date-Modified = {2017-09-07 16:17:44 +0000},
Journal = {Nature Biotechnology},
Number = {10},
Pages = {894--897},
Title = {The anatomy of successful computational biology software},
Volume = {31},
Year = {2013}
}
@misc{andersoncoursebook,
author = {Anderson, Brooke and Severson, Rachel},
title = {{R Programming for Research}},
howpublished = {\url{https://geanders.github.io/RProgrammingForResearch/}},
note = {Accessed: 2018-06-24}
}
@misc{andersonmastering,
author = {Peng, Roger and Kross, Sean and Anderson, Brooke},
title = {{Mastering Software Development in R}},
howpublished = {\url{https://bookdown.org/rdpeng/RProgDA/}},
note = {Accessed: 2018-06-24}
}
@misc{authoringdatacamp,
title = {{Authoring in DataCamp}},
howpublished = {\url{https://authoring.datacamp.com}},
note = {Accessed: 2018-06-24}
}
@article{baumer2015data,
Author = {Baumer, Ben},
Date-Added = {2017-10-14 23:35:30 +0000},
Date-Modified = {2017-10-14 23:35:30 +0000},
Journal = {The American Statistician},
Number = {4},
Pages = {334--342},
Publisher = {Taylor \& Francis},
Title = {A data science course for undergraduates: Thinking with data},
Volume = {69},
Year = {2015}}
@article{baumer2018lessons,
title={Lessons from between the white lines for isolated data scientists},
author={Baumer, Benjamin S},
journal={The American Statistician},
volume={72},
number={1},
pages={66--71},
year={2018}
}
@book{baumer2017modern,
Author = {Baumer, Benjamin S and Kaplan, Daniel T and Horton, Nicholas J},
Date-Added = {2017-10-10 22:33:09 +0000},
Date-Modified = {2017-10-10 22:33:09 +0000},
Publisher = {CRC Press},
address = {Boca Raton},
Title = {Modern Data Science with R},
Year = {2017}}
@article{begley2012drug,
title={Drug development: Raise standards for preclinical cancer research},
author={Begley, C Glenn and Ellis, Lee M},
journal={Nature},
volume={483},
number={7391},
pages={531},
year={2012}
}
@article{begley2015reproducibility,
title={Reproducibility in science: improving the standard for basic and preclinical research},
author={Begley, C Glenn and Ioannidis, John PA},
journal={Circulation research},
volume={116},
number={1},
pages={116--126},
year={2015}
}
@Manual{biobroom,
title = {biobroom: Turn Bioconductor objects into tidy data frames},
author = {Andrew J. Bass and David G. Robinson and Steve Lianoglou and Emily Nelson and John D. Storey and with contributions from Laurent Gatto},
year = {2017},
note = {R package version 1.8.0},
url = {https://github.com/StoreyLab/biobroom},
}
@misc{bookdownorg,
title = {Bookdown},
howpublished = {\url{https://bookdown.org}},
note = {Accessed: 2018-06-24}
}
@article{broman2018data,
title={Data organization in spreadsheets},
author={Broman, Karl W and Woo, Kara H},
journal={The American Statistician},
volume={72},
number={1},
pages={2--10},
year={2018}
}
@article{brown2018ten,
title={Ten quick tips for teaching programming},
author={Brown, Neil CC and Wilson, Greg},
journal={PLoS Computational Biology},
volume={14},
number={4},
pages={e1006023},
year={2018}
}
@article{bryan2018excuse,
title={Excuse me, do you have a moment to talk about version control?},
author={Bryan, Jennifer},
journal={The American Statistician},
volume={72},
number={1},
pages={20--27},
year={2018}
}
@article{cetinkaya2017infrastructure,
title={Infrastructure and tools for teaching computing throughout the statistical curriculum},
author={{\c{C}}etinkaya-Rundel, Mine and Rundel, Colin},
journal={The American Statistician},
number={In Press},
year={2017}
}
@misc{clearinghouse,
title = {{National Institute of General Medical Sciences: Clearinghouse for Training Modules to Enhance Data Reproducibility}},
howpublished = {\url{https://www.nigms.nih.gov/training/pages/clearinghouse-for-training-modules-to-enhance-data-reproducibility.aspx}},
note = {Accessed: 2018-06-24}
}
@Manual{countyfloods,
title = {countyfloods: Quantify United States County-Level Flood Measurements},
author = {Rod Lammers and Brooke Anderson},
year = {2017},
note = {R package version 0.0.2},
url = {https://CRAN.R-project.org/package=countyfloods},
}
@Manual{countyweather,
title = {countyweather: Compiles Meterological Data for U.S. Counties},
author = {Rachel Severson and Brooke Anderson},
year = {2016},
note = {R package version 0.1.0},
url = {https://CRAN.R-project.org/package=countyweather},
}
@book{cotton2017testing,
Author = {Cotton, Richard},
Date-Added = {2017-09-14 02:27:29 +0000},
Date-Modified = {2017-09-14 02:27:29 +0000},
Publisher = {CRC Press},
Title = {Testing R Code},
Year = {2017}}
@misc{datacamp,
title = {{DataCamp}},
howpublished = {\url{https://www.datacamp.com}},
note = {Accessed: 2018-06-24}
}
@article{ellis2018share,
title={How to share data for collaboration},
author={Ellis, Shannon E and Leek, Jeffrey T},
journal={The American Statistician},
volume={72},
number={1},
pages={53--57},
year={2018},
publisher={Taylor \& Francis}
}
@Manual{futureheatwaves,
title = {futureheatwaves: Find, Characterize, and Explore Extreme Events in Climate Projections},
author = {Brooke Anderson and Colin Eason and Elizabeth Barnes},
year = {2017},
note = {R package version 1.0.3},
}
@article{gentleman2004bioconductor,
title={Bioconductor: open software development for computational biology and bioinformatics},
author={Gentleman, Robert C and Carey, Vincent J and Bates, Douglas M and Bolstad, Ben and Dettling, Marcel and Dudoit, Sandrine and Ellis, Byron and Gautier, Laurent and Ge, Yongchao and Gentry, Jeff and others},
journal={Genome Biology},
volume={5},
number={10},
pages={R80},
year={2004}
}
@misc{gitpages,
title = {{GitHub Pages}},
howpublished = {\url{https://pages.github.com}},
note = {Accessed: 2018-06-24}
}
@article{godfrey2013statistical,
title={Statistical Software from a Blind Person's Perspective},
author={Godfrey, A Jonathan R},
journal={R Journal},
volume={5},
number={1},
pages = {73--79},
year={2013}
}
@article{goecks2010galaxy,
Author = {Goecks, Jeremy and Nekrutenko, Anton and Taylor, James},
Date-Added = {2017-10-10 21:05:42 +0000},
Date-Modified = {2017-10-10 21:05:42 +0000},
Journal = {Genome biology},
Number = {8},
Pages = {R86},
Publisher = {BioMed Central},
Title = {Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
Volume = {11},
Year = {2010}}
@article{goodman2016does,
title={What does research reproducibility mean?},
author={Goodman, Steven N and Fanelli, Daniele and Ioannidis, John PA},
journal={Science translational medicine},
volume={8},
number={341},
pages={341ps12--341ps12},
year={2016}
}
@misc{googleanalytics,
title = {{Google Analytics}},
howpublished = {\url{https://www.google.com/analytics/}},
note = {Accessed: 2018-06-24}
}
@misc{googleforms,
title = {Google Forms},
howpublished = {\url{https://www.google.com/forms/about}},
note = {Accessed: 2018-06-24}
}
@book{grolemund2016r,
Author = {Grolemund, Garrett and Wickham, Hadley},
Date-Added = {2017-09-07 15:49:24 +0000},
Date-Modified = {2017-09-07 15:49:24 +0000},
Publisher = {Hadley Wickham},
Title = {R for Data Science},
Year = {2016}}
@article{hicks2017guide,
Author = {Hicks, Stephanie C and Irizarry, Rafael A},
Journal = {The American Statistician},
Volume = {In Press},
Title = {A Guide to Teaching Data Science},
Year = {2017},
doi = {10.1080/00031305.2017.1356747}}
@article{hsieh2016inext,
Author = {Hsieh, TC and Ma, KH and Chao, Anne},
Date-Added = {2017-09-14 03:00:09 +0000},
Date-Modified = {2017-09-14 03:00:09 +0000},
Journal = {Methods in Ecology and Evolution},
Number = {12},
Pages = {1451--1456},
Publisher = {Wiley Online Library},
Title = {{iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)}},
Volume = {7},
Year = {2016}}
@article{huber2015orchestrating,
Author = {Huber, Wolfgang and Carey, Vincent J and Gentleman, Robert and Anders, Simon and Carlson, Marc and Carvalho, Benilton S and Bravo, Hector Corrada and Davis, Sean and Gatto, Laurent and Girke, Thomas and others},
Date-Added = {2017-10-10 20:55:14 +0000},
Date-Modified = {2017-10-10 20:55:14 +0000},
Journal = {Nature Methods},
Number = {2},
Pages = {115--121},
Title = {Orchestrating high-throughput genomic analysis with {Bioconductor}},
Volume = {12},
Year = {2015}}
@article{ioannidis2014increasing,
title={Increasing value and reducing waste in research design, conduct, and analysis},
author={Ioannidis, John PA and Greenland, Sander and Hlatky, Mark A and Khoury, Muin J and Macleod, Malcolm R and Moher, David and Schulz, Kenneth F and Tibshirani, Robert},
journal={The Lancet},
volume={383},
number={9912},
pages={166--175},
year={2014}
}
@article{kaplan2018teaching,
title={Teaching stats for data science},
author={Kaplan, Daniel},
journal={The American Statistician},
volume={72},
number={1},
pages={89--96},
year={2018},
publisher={Taylor \& Francis}
}
@inproceedings{krishnan2016towards,
title={Towards reliable interactive data cleaning: A user survey and recommendations},
author={Krishnan, Sanjay and Haas, Daniel and Franklin, Michael J and Wu, Eugene},
booktitle={Proceedings of the Workshop on Human-In-the-Loop Data Analytics},
pages={9},
year={2016},
organization={ACM}
}
@article{leek2015opinion,
title={Reproducible research can still be wrong: Adopting a prevention approach},
author={Leek, Jeffrey T and Peng, Roger D},
journal={Proceedings of the National Academy of Sciences},
volume={112},
number={6},
pages={1645--1646},
year={2015}
}
@book{lifesciencesR,
Author = {Irizarry, Rafael A. and Love, Michael I.},
Date-Added = {2017-10-10 22:35:36 +0000},
Date-Modified = {2017-10-10 22:36:24 +0000},
Publisher = {Chapman and Hall},
Title = {Data Analysis for the Life Sciences with R},
Year = {2016}}
@article{list2017ten,
Author = {List, Markus and Ebert, Peter and Albrecht, Felipe},
Date-Added = {2017-09-07 16:07:43 +0000},
Date-Modified = {2017-09-07 16:07:43 +0000},
Journal = {PLoS Computational Biology},
Number = {1},
Pages = {e1005265},
Title = {Ten simple rules for developing usable software in computational biology},
Volume = {13},
Year = {2017}
}
@article{lowndes2017our,
Author = {Lowndes, Julia S Stewart and Best, Benjamin D and Scarborough, Courtney and Afflerbach, Jamie C and Frazier, Melanie R and O'Hara, Casey C and Jiang, Ning and Halpern, Benjamin S},
Date-Added = {2017-10-14 23:32:45 +0000},
Date-Modified = {2017-10-14 23:32:45 +0000},
Journal = {Nature Ecology \& Evolution},
Number = {6},
Pages = {160},
Title = {Our path to better science in less time using open data science tools.},
Volume = {1},
Year = {2017}}
@article{marwick2018packaging,
title={Packaging data analytical work reproducibly using {R} (and friends)},
author={Marwick, Ben and Boettiger, Carl and Mullen, Lincoln},
journal={The American Statistician},
volume={72},
number={1},
pages={80--88},
year={2018}
}
@article{mcmurdie2013phyloseq,
Author = {McMurdie, Paul J and Holmes, Susan},
Date-Added = {2017-09-14 02:32:25 +0000},
Date-Modified = {2017-09-14 02:32:25 +0000},
Journal = {PloS one},
Number = {4},
Pages = {e61217},
Publisher = {Public Library of Science},
Title = {phyloseq: an {R} package for reproducible interactive analysis and graphics of microbiome census data},
Volume = {8},
Year = {2013}}
@article{mcnamara2016state,
Author = {McNamara, Amelia},
Date-Added = {2017-10-14 23:38:06 +0000},
Date-Modified = {2017-10-14 23:38:06 +0000},
Journal = {arXiv preprint arXiv:1610.00984},
Title = {On the State of Computing in Statistics Education: Tools for Learning and for Doing},
Year = {2016}}
@article{munafo2017manifesto,
title={A manifesto for reproducible science},
author={Munaf{\`o}, Marcus R and Nosek, Brian A and Bishop, Dorothy VM and Button, Katherine S and Chambers, Christopher D and du Sert, Nathalie Percie and Simonsohn, Uri and Wagenmakers, Eric-Jan and Ware, Jennifer J and Ioannidis, John PA},
journal={Nature Human Behaviour},
volume={1},
pages={0021},
year={2017}
}
@article{nih2016strategic,
Author = {{U.S. Department of Health and Human Services, National Institutes of Health}},
Title = {{NIH-Wide Strategic Plan, Fiscal Years 2016-2020: Turning Discovery
Into Health}},
Url = {https://www.nih.gov/sites/default/files/about-nih/strategic-plan-fy2016-2020-508.pdf},
Year = {2016},
note = {Accessed: 2018-06-24}
}
@article{nih2018data,
Author = {{U.S. Department of Health and Human Services, National Institutes of Health}},
Title = {{NIH Strategic Plan for Data Science}},
Url = {https://datascience.nih.gov/sites/default/files/NIH_Strategic_Plan_for_Data_Science_Final_508.pdf},
Year = {2018},
note = {Accessed: 2018-06-24}
}
@Manual{noaastormevents,
title = {noaastormevents: Explore NOAA Storm Events Database},
author = {Brooke Anderson and Ziyu Chen},
year = {2017},
note = {R package version 0.1.0},
url = {https://github.com/zailchen/noaastormevents},
}
@article{parker2017opinionated,
Author = {Parker, Hilary},
Date-Added = {2017-10-14 01:13:24 +0000},
Date-Modified = {2017-10-14 01:13:24 +0000},
Journal = {PeerJ Preprints},
Pages = {e3210v1},
Title = {Opinionated analysis development},
Volume = {5},
Year = {2017}}
@article{pathak2014rhadoop,
Author = {Pathak, Akshay Mittal Sharvanath and Bannard, Trevor},
Date-Added = {2017-10-10 21:03:27 +0000},
Date-Modified = {2017-10-10 21:03:27 +0000},
Journal = {R package},
Title = {Rhadoop: an improved execution environment for restricted map reduce programs},
Year = {2014}}
@article{pawlik2017developing,
Author = {Pawlik, Aleksandra and van Gelder, Celia WG and Nenadic, Aleksandra and Palagi, Patricia M and Korpelainen, Eija and Lijnzaad, Philip and Marek, Diana and Sansone, Susanna-Assunta and Hancock, John and Goble, Carole},
Date-Added = {2017-10-10 22:25:14 +0000},
Date-Modified = {2017-10-10 22:25:14 +0000},
Journal = {F1000Research},
pages = {ELIXIR-1040},
Publisher = {Faculty of 1000 Ltd},
Title = {Developing a strategy for computational lab skills training through {Software and Data Carpentry}: Experiences from the {ELIXIR Pilot} action},
Volume = {6},
Year = {2017}}
@article{peng2011reproducible,
title={Reproducible research in computational science},
author={Peng, Roger D},
journal={Science},
volume={334},
number={6060},
pages={1226--1227},
year={2011}
}
@article{pernet2015improving,
title={Improving functional magnetic resonance imaging reproducibility},
author={Pernet, Cyril and Poline, Jean-Baptiste},
journal={Gigascience},
volume={4},
number={1},
pages={15},
year={2015}
}
@article{piccolo2016tools,
Author = {Piccolo, Stephen R and Frampton, Michael B},
Date-Added = {2017-10-10 20:56:54 +0000},
Date-Modified = {2017-10-10 20:56:54 +0000},
Journal = {GigaScience},
Number = {1},
Pages = {30},
Publisher = {BioMed Central},
Title = {Tools and techniques for computational reproducibility},
Volume = {5},
Year = {2016}}
@incollection{brown2014reproducible,
title={Reproducible Bioinformatics Research for Biologists},
author={Brown, C Titus and Pyrkosz, Alexis Black and Preeyanon, Likit},
booktitle={Implementing Reproducible Research},
pages={205--238},
year={2014},
publisher={Chapman and Hall/CRC}
}
@article{ram2013git,
Author = {Ram, Karthik},
Date-Added = {2017-10-10 21:23:03 +0000},
Date-Modified = {2017-10-10 21:23:03 +0000},
Journal = {Source Code for Biology and Medicine},
Number = {1},
Pages = {7},
Title = {Git can facilitate greater reproducibility and increased transparency in science},
Volume = {8},
Year = {2013}}
@article{reviewer2017review,
Author = {Reviewer-Miller, Allan M},
Date-Added = {2017-10-14 23:37:30 +0000},
Date-Modified = {2017-10-14 23:37:30 +0000},
Journal = {ACM SIGACT News},
Number = {3},
Pages = {14--19},
Publisher = {ACM},
Title = {Review of {'R for Data Science: Import, Tidy, Transform, Visualize, and Model Data'} by {Hadley Wickham and Garrett Grolemund}},
Volume = {48},
Year = {2017}}
@article{RJ-2017-035,
Author = {Taylor Arnold},
Date-Added = {2017-09-14 02:49:28 +0000},
Date-Modified = {2017-09-14 02:49:28 +0000},
Journal = {{The R Journal}},
Volume = 9,
Number = 2,
pages = {248--267},
Title = {{A Tidy Data Model for Natural Language Processing using cleanNLP}},
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