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further_resources.Rmd
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further_resources.Rmd
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---
title: "Further Resources"
output: html_document
---
## Getting Help
- [Google it!](http://lmgtfy.com/?q=R+Error+in+library+there+is+no+package+called): Try Googling generalized versions of any error messages you get. That is, remove text that is specific to your problem (names of variables, paths, datasets, etc.). You'd be surprised how many other people have probably had the same problem and solved it.
- [Stack Overflow](http://stackoverflow.com/questions/tagged/r): There are over 100,000 questions tagged with "R" on SO. [Here are the most popular ones, ranked by vote](https://stackoverflow.com/questions/tagged/r?sort=votes). Always search before asking, and make a [reproducible example](http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example/5963610#5963610) if you want to get useful advice. This is a minimal example that allows others who are trying to help you to see the error themselves.
- [Bioconductor Support Site](https://support.bioconductor.org/): Like SO, but specifically for Bioconductor-related questions.
- Read package vignettes. For example, see the [dplyr CRAN page](https://cran.r-project.org/web/packages/dplyr/index.html), scroll about halfway down to see the [introduction to dplyr](https://cran.r-project.org/web/packages/dplyr/vignettes/introduction.html) vignette.
- [Biostars RNA-seq](https://www.biostars.org/) Q&A section.
## Learning and teaching R
- [TryR](http://tryr.codeschool.com/): An interactive, browser-based R tutor
- [Swirl](http://swirlstats.com/): An R package that teaches you R (_and statistics!_) from within R
- [Kelly Black's R Tutorial](https://www.cyclismo.org/tutorial/R/index.html)
- [Jenny Bryan's Stat 545 "Data wrangling, exploration, and analysis with R" course material](https://stat545-ubc.github.io/): An excellent resource for learning R, dplyr, and ggplot2
- [DataCamp's free introduction to R](https://www.datacamp.com/courses/free-introduction-to-r)
- [More DataCamp courses](https://www.datacamp.com/courses).
- [RStudio's printable cheat sheets](https://www.rstudio.com/resources/cheatsheets/)
- [Rseek](http://rseek.org/): A custom Google search for R-related sites
- Bioconductor [vignettes](https://www.bioconductor.org/help/package-vignettes/), [workflows](https://www.bioconductor.org/help/workflows/), and [course/conference materials](https://www.bioconductor.org/help/course-materials/)
## dplyr resources
- [The dplyr vignette](https://cran.rstudio.com/web/packages/dplyr/vignettes/introduction.html)
- [A longer dplyr tutorial with video and code](http://www.dataschool.io/dplyr-tutorial-for-faster-data-manipulation-in-r/)
- [The dplyr tutorial from the HarvardX Biomedical Data Science MOOC](http://genomicsclass.github.io/book/pages/dplyr_tutorial.html)
- [A dplyr cheat sheet from RStudio](https://www.rstudio.com/wp-content/uploads/2015/02/data-wrangling-cheatsheet.pdf)
## ggplot2 resources
- [The official ggplot2 documentation](http://docs.ggplot2.org/)
- [The ggplot2 book](http://amzn.to/1akjqsR), edition 1, by the developer, Hadley Wickham
- [New version of the ggplot2 book, freely available on GitHub](https://github.com/hadley/ggplot2-book)
- [The ggplot2 Google Group](https://groups.google.com/d/forum/ggplot2) (mailing list, support forum)
- [LearnR](http://learnr.wordpress.com/): A blog with a good number of posts describing how to reproduce various kind of plots using ggplot2
- [SO questions tagged with ggplot2](http://stackoverflow.com/questions/tagged/ggplot2)
- [A catalog of graphs made with ggplot2, complete with accompanying R code](http://shinyapps.stat.ubc.ca/r-graph-catalog/)
- [RStudio's ggplot2 cheat sheet](https://www.rstudio.com/wp-content/uploads/2015/05/ggplot2-cheatsheet.pdf)
## Markdown / RMarkdown resources
- [Basic Markdown + RMarkdown reference](http://bioconnector.github.io/markdown)
- In-browser markdown editors:
- Minimal: [bioconnector.github.io/markdown-editor](http://bioconnector.github.io/markdown-editor)
- Better: [stackedit.io](http://stackedit.io), [dillinger.io](http://dillinger.io)
- [A good markdown reference](http://commonmark.org/help/)
- [A good 10-minute markdown tutorial](http://commonmark.org/help/tutorial/)
- [RStudio's RMarkdown Cheat Sheet](https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf) and [RMarkdown Reference Sheet](https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf)
- [The RMarkdown documentation](<http://rmarkdown.rstudio.com/>) has an excellent [getting started guide](http://rmarkdown.rstudio.com/lesson-1.html), a [gallery of demos](http://rmarkdown.rstudio.com/gallery.html), and several [articles](http://rmarkdown.rstudio.com/articles.html) illustrating advanced usage.
- [The knitr website](<http://yihui.name/knitr/>) has lots of useful reference material about how knitr works, [options](http://yihui.name/knitr/options/), and more.