Instructors

Life Sciences Research Unit
University of Luxembourg

Aim

Replace R base functions by the tidyverse. Adopt Hadley Wickham philosophy, take each step of data science and simplify the tools. Keeping what make them helpful and removing inconsistent and historic behaviors.

Summary in one picture, by David Robinson

Install tutorial

visit the dedicated page

Preliminary program

June 2nd morning, for complete beginner

Lecture ~ 45 minutes
hands-on Rstudio
  • Practical: html / pdf

  • Practical solution: html / pdf

  • practice on a small dataset
  • reading, specify locales and avoid factor conversions
  • tidying data
  • transform wide / long format
  • detect and remove mistakes
  • plotting with ggplot2
  • introduction to the grammar of graphics
  • use aesthetics to map variables to columns
  • explore the world of geom_*

  • faceting for 1 or 2 variables

June 2nd afternoon, intermediate level

small presentation ~ 30 minutes - dplyr
microarray hands-on
  • Practical: html / pdf

  • Practical solution: html / pdf

  • public dataset of mRNA / mir from GEO using bioconductor package
  • tidying data, split text
  • merging annotation tables

  • Fit linear models to mRNA/mir expression using dplyr::do()

June 3rd morning, advanced user

small presentation ~ 20 minutes

the interactive version is accessible only inside the university network.

practical with yeast data.
  • Practical: online

  • Practical solution: online

  • tidying data
  • performing thousands of linear regression
  • tidying / ranking models using functional programming using purrr and nested data frames
  • animate time series using gganimate
  • viz comparison using UpSetR

  • interactive input using embedded shiny in rmarkdown

Practical information

Please, do bring your laptop as no computer will be available. Everyone should have one according to the survey.

Schedule

Day Session Start End
June 2nd 2016 Beginner 08:30 12:30
June 2nd 2016 Intermediate 13:30 18:00
June 3rd 2016 Advanced 08:00 12:15

Hot & cold drinks will be served during the morning breaks.

Location

Campus Belval, Maison du Savoir in Room 2.220, second floor.

Inside

About

Of note, all material was written in rmarkdown (.Rmd) using Rstudio.

You can download the Rmd for each slides / practical by changing the extension. For example lecture_day1-beginner.Rmd and open in rstudio.

Behind the scene, pandoc does all the conversion.