resources.md

title	author	date	layout	sidebar	tag	categories
Resources	Luke Johnston	2015-04-12	page	false	Resources	Resources

Content:

• Reproductibility
• Git
• R
• SAS

Reproducibility

• Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, et al. (2014). Best practices for scientific computing. PLoS Biol. 12(1):e1001745. http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745
• Sandve GK, Nekrutenko A, Taylor J, Hovig E (2013) Ten Simple Rules for Reproducible Computational Research. PLoS Comput Biol 9(10): e1003285. http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285
• Alsheikh-Ali, Qureshi W, Al-Mallah MH, Ioannidis JP. (2013). Public availability of published research data in high-impact journals. PLoS One. 6(9):e24357. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024357
• Laine C, Goodman SN, Griswold ME, Sox HC. (2007). Reproducible research: moving toward research the public can really trust. Ann Intern Med. 146(6):450-3. (Closed access)
• Peng RD, Dominici F, Zeger SL (2006). Reproducible epidemiologic research. Am J Epidemiol. 163(9):783-789. http://aje.oxfordjournals.org/content/163/9/783.full
• http://reproducibleresearch.net/ (an informative blog)
• http://blogs.plos.org/everyone/2012/08/14/plos-one-launches-reproducibility-initiative/ (Announcement of PLOS ONE 2012 Reproducibility Initiative)
• http://www.nature.com/nature/focus/reproducibility/
• http://ropensci.org/blog/2014/06/09/reproducibility/
• http://biostatistics.oxfordjournals.org/content/10/3/405.full
• http://www.sciencemag.org/content/314/5807/1856.full
• http://stats.stackexchange.com/questions/14999/how-are-we-defining-reproducible-research
• http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003285

Git

• Visual guide to Git
• Official Git documentation and introduction
• Other documentation (nice and clean)
• Hands-on tutorial, with web-based terminal
• A tutorial from a scientists perspective
• An introduction to Git for researchers
• Software carpentry lesson material for Git
• A scientists arguments and evidence for using Git
• Simpler first-steps guide
• Reference pages for all git commands
• Interactive, visual tutorial on branching
• StackOverflow questions and answers on Git

R

• RStudio Cheat Sheets

Basics of R

• CRAN website
• CRAN R Reference Card
• Interactive R tutorial
• R in a Nutshell

Data wrangling

• Common and frequently used commands in R
• Data frames in dplyr
• Introduction to dplyr
• Cheatsheet for dplyr and tidyr
• Merging two dataframes using dplyr
• Introduction to tidyr
• Shorter intro to tidyr
• Regular expressions
• Regular expression symbol meaning
• dplyr with databases in SQL and other formats

R Markdown

Short guides/help:

• R Markdown Cheat Sheet
• Markdown basics
• Code chunk options brief
• Bibliographies and citations
• Creating HTML documents (YAML options)
• Creating Word documents (YAML options)
• Using the captioner package

Detailed guides/help:

• R Markdown site
• R Markdown more complete reference sheet
• More detailed markdown reference (pandoc)
• Pandoc Markdown website
• knitr website
• Code chunk options detailed
• Customization of markdown tables (pander)
• For installation or documentation of LaTeX

SAS

ODS

• SAS ODS Output Support

Other resources

• http://www.stackoverflow.com
• http://stats.stackexchange.com
• http://software-carpentry.org/