title	author	date	output
SISBID 2016 Module 3: Reproducible Research	Keith Baggerly	July 18-20, 2016	html_document

This module is part of the Summer Institute in Statistics for Big Data

Taught by
Keith A. Baggerly
[email protected]
and
Roger Peng
[email protected]

Course Goals

• Course Goals
  pdf (100K), html (630K), MS Word (12K), Rmd Source (5K)

Homeworks

• Homework
  pdf (100K), html (630K), Rmd Source (3K)
• Supplementary Data for Homework
  .RData (75M)
• About the Homework Data
  pdf (160K), html (650K), Rmd Source (12K)

Cheat Sheets (idea stolen from Karl Broman)

These are from RStudio's list

• Rmarkdown; there's also a reference guide
• Package Development/Devtools

This is from GitHub

• Git/GitHub

Course Syllabus and Lecture Materials

Day 1, Jul 18, 2016

Session 1, 8:30-10

• 10 minute intro pdf (260K) printable pdf (260K)

• General Intro to RR (75 min) printable pdf (3.4M)

• Getting crushed on the Internet

• Making your work reproducible

Session 2, 10:30-12

• The Duke Saga (45 min) pdf (3.6M) printable pdf (3.6M)
• Using R markdown (30 min) pdf (800K)
• Begin Day 1 Homework (draft Rmd file, generate html, pdf)

Session 3, 1:30-3

• Assembling R Packages (1hr) pdf (163K) printable pdf (162K)
• RStudio R package pre-flight check list
• More Day 1 Homework (build a toy package)

This session will be a mix of lecture and live demo.

Session 4, 3:30-5

• Exciting Big Data/Hwk Data Intro (15 min) pdf (4M) printable pdf (4M)
• More Day 1 Homework (explore TCGA, Tumor Portal, package)

This session will be a mix of lecture and live demo.

• Day 1 Feedback (5 min)

Day 2, Jul 19, 2016

Session 5, 8:30-10

• Discussion of Readings (15 min)
• Problems with RR (45 min) pdf (2.5M) printable pdf (2.5M)
• Git/GitHub, Part 1 (30 min) pdf (4.7M) printable pdf (4.7M)

This session will be a mix of lecture and live demo.

Session 6, 10:30-12

• Git/GitHub, Part 2 (45 min, continued) pdf (1.7M) printable pdf (1.7M)
• Begin Day 2 Homework (put a toy package on github, share)

This session will be a mixture of lecture and live demo.

Session 7, 1:30-3

• Prevention vs Cure (45 min) printable pdf (1.7M)

• ROC Curves of Science

• More Day 2 Homework (responding to changes suggested)

Session 8, 3:30-5

• More Day 2 Homework (sharing real data analyses, incorporating batch effects)
• Day 2 Feedback (5 min)

Day 3, Jul 20, 2016

Session 9, 8:30-10

• Discussion of Readings (15 min)
• Writing Reports (45 min) pdf (150K) printable pdf (150K)
• Begin Day 3 Homework (revising vignettes as reports)

Session 10, 10:30-12

• More Day 3 Homework
• Final Class Discussion (30 min)

Recommended Reading/Browsing

General

• Christopher Gandrud, Reproducible Research with R and Rstudio, 2e (2015)
• Hadley Wickham, R Packages (2015)
• Yihui Xie, Dynamic Documents with R and knitr, 2e (2015)

Karl Broman's Tools for RR Course

Day 1

• Potti et al (2006)
• our letter
• the response
• Brad Perez's letter

Day 2

• Petricoin et al, Lancet (2002)
• Baggerly et al, Bioinformatics (2004)
• Leek et el, Nat Rev Genet (2010)