| 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
kabagger@mdanderson.org
and
Roger Peng
rdpeng@jhu.edu
- Course Goals
pdf (100K), html (630K), MS Word (12K), Rmd Source (5K)
- 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
-
10 minute intro pdf (260K) printable pdf (260K)
-
General Intro to RR (75 min) printable pdf (3.4M)
- 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)
- 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.
- 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)
- 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.
- 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.
-
Prevention vs Cure (45 min) printable pdf (1.7M)
-
More Day 2 Homework (responding to changes suggested)
- More Day 2 Homework (sharing real data analyses, incorporating batch effects)
- Day 2 Feedback (5 min)
- Discussion of Readings (15 min)
- Writing Reports (45 min) pdf (150K) printable pdf (150K)
- Begin Day 3 Homework (revising vignettes as reports)
- More Day 3 Homework
- Final Class Discussion (30 min)