Course Info

• Instructor: Seong-Hwan Jun.
• TAs:
  • Hanwen Li. Office hour on Thursday 1-2 pm.
  • Abby Nguyen. Office hour on Monday 12:15-1:15 pm.
• Syllabus

Resources

• R4DS: R for Data Science (2e)
• ADVR: Advanced R
• MSMB: Modern Statistics for Modern Biology
• RPKG: R Packages (2e)
• HGWR: Happy Git with R
• OHGA: Orchestrating high-throughput genomic analysis with Bioconductor
• OSCA: Orchestrating Single Cell Analysis with Bioconductor
• G4S: Git for scientists
• TSG: Tidyverse style guide

Homeworks

• HW2.
• HW1.

Labs

• LB06.
• LB05.

  library(vroom)
  crashes = vroom('data/ny_collisions_2018_2019.csv.gz')
  

• LB04.
• LB03
• LB02
• LB01
• LB00

Quizzes

• Quiz3
• Quiz2
• Quiz1

Exercises

• Git branching and rebase exercise
• Git merge conflict exercise

Course Schedule

Oct 8: Linear models

• Slides.
• Code and data.

Oct 3: Functional programming and styles

• Functional programming
• Styles
• References: ADVR Ch. 9-11.

Oct 1: Functions (Guest lecture by Don Harrington)

• Slides

Sep 26: Functions

• Slides
• References
  • Functions: R4DS Ch. 25
  • Functionals: ADVR Ch. 9
  • Functionals: ADVR Ch. 10

Sep 24: Strings and regular expressions

• stringr Slides
  • Code and data
• References
  • Strings: R4DS Ch. 14
  • Regular expressions: R4DS Ch. 15

Sep 19: Factors, dates, and times

• forcats and lubridate slides
  • Code and data
• References
  • Factors: R4DS Ch. 16
  • Dates and times: R4DS Ch. 17

Sep 17: Data wrangling II

• tidyr slides
  • Code and data
• data.table slides
• References
  • Data tidying: R4DS Ch. 5
  • Joins: R4DS Ch. 19.
  • vignettes for data.table

Sep 12: Class cancelled

Conference in honor of David Oakes: https://www.urmc.rochester.edu/biostat/events/oakes-conference

Sep 10: Data wrangling I

• dplyr slides
  • Code and data
• References
  • Data transform: R4DS Ch. 3
  • Transform logical vectors: R4DS Ch. 12
  • Transform numbers: R4DS Ch. 13

Sep 5: Visualization

• ggplot2 slides
• References
  • Data visualization: R4DS Ch. 1
  • Grammar of graphcis: R4DS Ch. 9
  • Exploratory data analysis: R4DS Ch. 10
  • Communication: R4DS Ch. 11
• Quiz 1: Answer Exercise 1.2.5 questions 1-8, 10 from R4DS.

Sep 3: Data import

• Intro to tidyverse slides
• readr slides
  • Code and Data
• References
  • Data import: R4DS Ch. 7

Aug 29: R language fundamentals

• Data types slides
  • Code
  • Cat lovers data
• Indexing slides
  • Code
• Memory slides
• References
  • Names and values: ADVR Ch. 2
  • Data types: ADVR Ch. 3
  • Indexing: ADVR Ch. 4

Aug 27: Meet the toolkit

• Intro slides
• Toolkits slides
• References
  • Introduction to R and RStudio: R4DS Ch. 2, R4DS Ch. 6
  • Reproducibility:
    • git (HGWR Ch. 4-14)
    • Quarto (R4DS Ch. 28)