5 May 2017

Learning objectives

So much for the tidyverse

  • Reading data
  • Tidy data
  • Manipulation
  • Functional programming
  • Tidying model objects
  • Consistent and compact data analysis using tidy verse
R tidyverse workshop

Missing features

R tidyverse workshop

dplyr case_when()

Great vectorise multiple if and else if statements

summary(iris$Petal.Length)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.600   4.350   3.758   5.100   6.900 
iris %>%
  as_tibble() %>%
  mutate(
    petal_length_cat = case_when(
      Petal.Length < 2 ~ "super_small",
      Petal.Length < 4 ~ "small",
      Petal.Length < 6 ~ "big",
      TRUE ~ "very_big")) %>%
  ggplot(aes(x = Petal.Length,
             fill = petal_length_cat)) +
  geom_density(alpha = 0.6)

R tidyverse workshop

ELIXIR

ELIXIR is a bioinformatics infrastructure programme

  • Hub at the EBI and national nodes
  • Platforms
    • Data
    • Tools
    • Compute
  • Interoperability
  • Training

Across Europe

R tidyverse workshop

Elixir-Luxembourg

Focus

  • LCSB is the national node for Luxembourg ELIXIR-LU
  • Focus on translational medicine
R tidyverse workshop

ELIXIR-LU training in Luxembourg

Training focus

Training plan

  • On-site training and hands-on training courses
    • User training of TMDC and tranSMART
    • Curation of clinical data and integration to tranSMART
    • Basic bio-medical research IT training for researchers
    • Data management at the bench – from Excel to Tidy Data in statistical analysis platform
    • Basic bioinformatics, reproducible pipelines and reproducible analysis
R tidyverse workshop

Future courses

Upcoming events

  • Advanced git training
    • 2017-05-12, 9:00 @ LCSB
  • ELIXIR-LU launch event
    • 2017-09-07, 9:00
  • Big data in healthcare meeting
    • 2017-10-04
  • TMDC and tranSMART courses will be scheduled in May
  • Smaller course to be arranged on shorter schedule
  • Focus on development of advanced courses

Opportunities

R tidyverse workshop

Acknowledgments

tidyverse and course material

  • Hadley Wickham
  • Robert Rudis
  • Jennifer Bryan
  • Ian Lyttle
  • David Robinson
  • Bruno Rodrigues
  • Jeremy Stanley

Organization ELIXIR-LU

  • Reinhard Schneider
  • Wei Gu
  • Marie-Laure Magnani
  • Anya Androsova
R tidyverse workshop