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}

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}

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}

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  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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  year = {2004},
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  publisher = {Association for Computing Machinery ({ACM})},
  volume = {47},
  number = {11},
  pages = {58--63},
  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},
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  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},
    url  = {https://www.elegantthemes.com/blog/wordpress/how-to-comment-your-code-like-a-pro-best-practices-and-good-habits},
}

@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},
}

@article{Kumar2007,
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  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},
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  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,
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  url = {https://doi.org/10.1186/s13059-019-1649-8},
  year = {2019},
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  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},
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  title = {Challenges and recommendations to improve the installability and archival stability of omics computational tools},
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}

@website{Meza2018,
    author = {Frank Meza},
    year = {2018},
    title = {The Value of Code Documentation},
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}

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  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]
},
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  doi = {10.12688/f1000research.29032.1}
}

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    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,
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    title = {Usability Testing 101},
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}

@article{Mulder2018,
  doi = {10.1371/journal.pcbi.1005772},
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  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,
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  url = {https://doi.org/10.1371/journal.pcbi.1002554},
  year = {2012},
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  volume = {8},
  number = {7},
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  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}
}

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    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/},
}