R Language Tips & Tricks

• Hadley Wickham’s Ask Me Anything (AMA)
• Organizing Data in R (Doug Bates)
• R Easy-To-Use Wraps
• R Beginning & Advanced Guides & Tips
• Visualization with R
• Building R Packages
• R, Bioconductor, Biology & Bioinformatics
• R Resources & Archives

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Organizing Data in R (Doug Bates)

• Download “Organizing.Rmd” File from Box
• Organizing.Rmd: R MarkDown
• Organizing.md: MarkDown after R Without Figures
• Organizing.html: HTML Version
• Doug Bates GitHub Repository for Stat 692 (Fall 2014)

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R Easy-To-Use Wraps

• RStudio (IDE for R)
• knitr, markdown, pandoc & Sweave
• R Commander (Rcmdr)
• Sage Cell Server (Runs R Online) | see Jed Frees’s Course, Ch 6: GLIM Example with SageCell
• Seamless R & C++ Integration (Rcpp) (more advanced topic)
• Pretty Quick R (pqR) (faster version of R)
• Roxygen: Documentation System for R Literate Programming

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R Beginning & Advanced Guides & Tips

• R Documentation
• R Markdown Cheat Sheet
• R Data Import/Export
• Karl Broman’s Introduction to R
• Tom Lumley’s UW-Seattle Short Course on R
• John Gillett’s Introductory Data Analysis with R (UW Stat 327)
• Roger Peng’s Computing for Data Analysis (Coursera)
• R Training Videos
  • Google Developers’ Intro to R (youtube videos)
  • Lynda.com: Up and Running with R
  • R, knitr, Reproducible Research (Roger Peng)
  • Using R for Graphics Programming (Stanford Lane Library)
• RStudio Training
• Google’s R Style Guide
• R Software Introduction for Stat 571 | R Appendices for Course Notes
• Advanced Programming in R (Hadley Wickham)
• Knitr Reproducible Research
• Frank Harrell’s Statistical Reporting Tips

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R, Bioconductor, Biology & Bioinformatics

• Robert Gentleman (2008) Bioinformatics with R. Chapman & Hall/CRC. ISBN 1-420-06367-7. R Publications
• Computing for Statistical Genetics (Ken Rice & Tom Lumley’s SISG Course)
• Advanced R Programming for Bioinformatics (Ken Rice & Tom Lumley’s SISG Course)
• Interactive graphics for high-dimensional genetic data (Karl Broman)
• Thirteen years of R/qtl: Just barely sustainable

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R Resources & Archives

• R Frequently Asked Questions
• The R Project
• R Wiki
• R Bloggers: News & Tutorials
• inside-R: A Community Site for R
• Quick-R (StatMethods)
• Software for Exploratory Data Analysis and Statistical Modelling with R (Weka Learn Studios)
• r4stats: Analyzing the World of Analytics
• Comprehensive R Archive Network (CRAN)
• Bioconductor: Open Source Software for Bioinformatics
• R Forge
• Trending R Repositories in GitHub
• Revolution Analytics: R for the Enterprise (Blog)
• R User Groups
  • MadUseR (Madison R User Group)