teaching
Current courses
Biomedical data science scholarly literature (BMI 881, Fall 2023)
Biomedical data science professional skills (BMI 883/884, Fall 2023)
Short courses
Analysis of BXD mouse lines with R/qtl2
Complex Trait Community meeting, San Diego, CA (June 9, 2019)
https://github.com/kbroman/Teaching_CTC2019
Jupyter notebook: 
RStudio:
2nd International Workshop on Advanced R and R/qtl
ICRISAT, Patancheru, Andhra Pradesh, India (Dec 3-7, 2018)
https://github.com/kbroman/icrisat2018
Reproducible Research Workshop
Reproducible Research Workshop, Summer Institute in Statistics for Big Data, Seattle, WA (16-18 July 2018)
Reproducible Research Workshop, Summer Institute in Statistics for Big Data, Seattle, WA (17-19 July 2017)
R/qtl and R/qtl2 workshop
R/qtl and R/qtl2 workshop, Complex Trait Community meeting, Memphis, TN (13 June 2017)
Data Carpentry
UW-Madison Madison, WI (27-28 Aug 2018)
- Course materials
- GitHub repository: web site | R lessons
UW-Madison Madison, WI (4-5 Jun 2018)
- Course materials
- GitHub repository: web site | R lessons
UW-Madison Madison, WI (8-9 Jan 2018)
- Course materials
- GitHub repository: web site | R lessons
National Society of Black Engineers Professional Development Conference Chicago, IL (28 Sept 2017)
- Course materials
- GitHub repository: web site | R lessons
UW-Madison Madison, WI (19-20 June 2017)
- Course materials
- GitHub repository: web site | R lessons
UW-Madison, Madison, WI (10-11 January 2017)
- Course materials
- GitHub repository: web site | R lessons
UW-Madison, Madison, WI (23-24 August 2016)
- Course materials
- GitHub repository: web site | R lessons
UW-Madison, Madison, WI (1-2 June 2016)
- Course materials
- GitHub repository: web site | R lessons
Software Carpentry
UW-Madison (for Social Scientists), Madison, WI (3-4 June, 2015)
Washington State University, Pullman, WA (27-28 April 2015)
UW-Madison, Madison, WI (25-26 August 2014)
R/qtl workshop at Texas A&M, 2 Sep 2015
- Introduction to QTL mapping: pdf | b/w pdf, 2 slides per page
- Interactive illustrations EM algorithm | LOD curves | Permutation test
- Multiple QTL mapping: pdf | b/w pdf, 2 slides per page
- R/qtl laboratory: pdf | code
- Videos:
Short course on Systems Genetics at The Jackson Lab
Oct 16-Oct 22, 2016
- Introduction to QTL mapping: pdf
- Interactive illustrations: EM algorithm | LOD curves | Permutation test
- Special topics: pdf
- Multiple QTL mapping: pdf
- Multivariate QTL mapping: pdf
- R/qtl laboratory: pdf (50k) | code
- R/qtlcharts: user guide
Sep 27-Oct 3, 2015
- Introduction to QTL mapping: pdf | b/w pdf, 2 slides per page
- Interactive illustrations EM algorithm | LOD curves | Permutation test
- Multiple QTL mapping: pdf | b/w pdf, 2 slides per page
- R/qtl laboratory: pdf (50k) | code
- R/qtlcharts: user guide
Sep 27-Oct 4, 2014
- Introduction to QTL mapping: pdf | b/w pdf, 2 slides per page
- Interactive illustrations EM algorithm | LOD curves | Permutation test
- A few slides on Haley-Knott regression: pdf | b/w pdf, 2 slides per page
- Multiple QTL mapping: pdf | b/w pdf, 2 slides per page
- R/qtl laboratory: pdf (50k) | code
Sep 8-14, 2013
- Introduction to QTL mapping: pdf (382k)
- Multiple QTL mapping: pdf (5.2M)
- R/qtl laboratory: pdf (50k) | code
Oct 28-Nov 4, 2012
- Introduction to QTL mapping: pdf (381k)
- Multiple QTL mapping: pdf (5.2M)
- R/qtl laboratory: pdf (50k) | code
Oct 2-9, 2011
- Introduction to QTL mapping: pdf (1.2M)
- Multiple QTL mapping: pdf (4.9M)
- R/qtl laboratory: pdf (51k) | code
Sep 19-25, 2010
- Introduction to QTL mapping: pdf (268k)
- Multiple QTL mapping: pdf (4.8M)
- R/qtl laboratory: pdf (51k) | code
Oct 19-25, 2009
- Introduction to QTL mapping: pdf (268k)
- Multiple QTL mapping: pdf (4.8M)
- R/qtl laboratory: pdf (51k) | code
Sep 23-29, 2008
- Introduction to QTL mapping: pdf (268k)
- Multiple QTL mapping: pdf (813k)
- R/qtl laboratory: pdf (138k) | code
Short course on Complex Trait Analysis at The Jackson Lab
Oct 11-17, 2007
- Introduction to QTL mapping: pdf (4.2M)
- R/qtl laboratory: pdf (125k) | code
Sep 16-22, 2006
- Introduction to QTL mapping: pdf (491k)
- R/qtl laboratory: pdf (69k) | code
Oct 5-11, 2005
- Introduction to QTL mapping: pdf (453k)
- R/qtl laboratory: pdf (69k) | code
Sep 16-22, 2004
- Introduction to QTL mapping: pdf (460k)
- R/qtl laboratory: pdf (69k) | code
Oct 9-15, 2003
- Introduction to QTL mapping: pdf (477k)
- R/qtl laboratory: pdf (54k) | code
Sep 18-24, 2002
- Statistics Overview: pdf (552k)
- Introduction to QTL mapping: pdf (488k)
Training course on field trial & QTL analysis using R & R/qtl
ICRISAT, Patancheru, Andhra Pradesh, India (Dec 3-6, 2012)
- Introduction to QTL mapping: [pdf (381k) | b/w pdf, 2 slides per page]
- Multiple QTL mapping: [pdf (4.9M) | b/w, 2 slides per page]
- R/qtl laboratory: [pdf (91k) | code]
NeuroproMiSe training course in genetic analysis and bioinformatics
Lund, Sweden (Jan 8-12, 2007)
- Interval mapping: [ lecture | handout ]
- AIL, RIL, RIX, HS, CC, CSS: [ lecture | handout ]
- Multiple QTL mapping: [ lecture | handout ]
- A brief tour of R/qtl: [ handout | code | additional functions ]
Summer Institute in Statistical Genetics, QTL Mapping II module
(formerly at NC State University, now held at the University of
Washington, Seattle)
Summer, 2006
- Introduction: pdf (280k)
- Model selection: pdf (243k)
- HMMs and the pseudomarker algorithm: pdf (1143k)
- R/qtl lab: pdf (70k) | code
Summer, 2005
- Introduction: pdf (668k)
- Model selection: pdf (51k)
- HMMs and the pseudomarker algorithm: pdf (1160k)
- R/qtl lab: pdf (68k) | code
Summer, 2004
- Introduction: pdf (638k)
- Model selection: pdf (51k)
- HMMs and the pseudomarker algorithm: pdf (1161k)
- R/qtl lab: pdf (67k) | code
Summer, 2003
- Introduction: pdf (331k)
- Model selection: pdf (76k)
- HMMs and the pseudomarker algorithm: pdf (1186k)
- R/qtl lab: pdf (69k)
Summer, 2002
- Introduction: pdf (755k)
- HMMs and the pseudomarker algorithm: pdf (1312k)
- Model selection: pdf (285k)
- R/qtl description/demo: pdf (24k)
Miscellaneous lectures
BMI/Stat 877 (Statistical methods for molecular biology), Spring 2022
- QTL mapping in multi-parent populations
Hort 615 (Genetic mapping)
QTL mapping in MAGIC populations with
R/qtl2
BMI 773 (Clinical research informatics)
-
Steps toward reproducible research
-
Exploratory data analysis
My experiences in statistical consulting
Statistical Consulting course, Department of Statistics, UW–Madison
Experimental design, basic statistics, and sample size determination for animal-based research
Enhancing Humane Science/Improving Animal Research course
Center for Alternatives
to Animal Testing, Johns Hopkins University
- Presentation: [ppt (1.2M)]
- Handout: [color pdf (5.1M) | B/W pdf (4.1M)]
- Video
Recombination and linkage
NS 881 (Dale Schoeller)
Department of Nutritional Sciences, University of Wisconsin - Madison
20 Feb 2008: [ ppt (2.2M) | pdf (1.1M) ]
PHS 904 Genetic Epidemiology (Engelman)
Population Health Sciences, University of Wisconsin - Madison
24 Jan 2008: [ ppt (3.8M) | pdf (1.3M) ]
Identifying QTL in experimental crosses
Advanced Topics in Human Genetics (Reeves and Feinberg)
Human Genetics, Johns Hopkins School of Medicine
9 Apr 2007: pdf (2.2M)
27 Feb 2006: pdf (461k)
28 Feb 2005: pdf (461k)
25 Feb 2004: pdf (461k)
27 Feb 2003: pdf (475k)
12 Feb 2002: pdf (750k)
16 Feb 2001: pdf (587k)
18 Feb 2000: pdf (587k)
Hopkins Biostatistics Student Computing Club
Mathematica
27 Apr 2007: [pdf (70k) | b/w pdf (77k) |
Code]
How to build a web page
8 Dec 2006: [ppt (1.0M) | pdf (618k)]
11 Nov 2005: [ppt (1.1M) | pdf (618k)]
Perl for human linkage analysis
Biocomputing I: Perl for bioinformatics (Pineda)
Biostatistics, Johns Hopkins Bloomberg School of Public Health
26 Oct 2005: pdf (42k)
6 Dec 2004: pdf (42k)
24 Oct 2003: pdf (42k)
14 May 2003: pdf (42k)
Former courses at UW-Madison
Advanced data analysis (BMI 826, Spring 2020)
Biomedical data science scholarly literature (BMI 882, Spring 2023)
Biomedical data science professional skills (BMI 884, Spring 2023)
Statistical methods for molecular biology (Stat 877), with many others (Spring 2019)
- Introduction to QTL mapping
- R/qtl script
- Interactive graphs: EM algorithm | LOD curves and QTL effects | permutation test
- Multi-parent populations
- Steps toward reproducible research
- Homework: [assignment (pdf) | data (csv) | solutions (html) | source (Rmd)]
Tools for reproducible research (BMI 826-003; Spring, 2016)
Plant breeding and plant genetics seminar (Agronomy 957; Spring, 2018)
Statistical methods for QTL mapping (BMI 826-001; Fall, 2012)
GAW 17 course (Pop Health 904 Sec 003), with many others
Introductory applied statistics for the life sciences (Stat 371)
Courses taught at Johns Hopkins
Special topics in genetics and genomics (140.668)
Statistics for laboratory scientists (140.615-616)
Statistical computing (140.776)
- Coding practices: [pdf (35k) | books]
- C Programming I: [pdf (56k) | books | Example code (c_code_1.tgz)]
- C Programming II: [pdf (57k) | Example code (c_code_2.tgz)]
- C Programming III: [pdf (14k) | Example code (c_code_3.tgz)]