| layout | title | description |
|---|---|---|
page |
teaching |
Karl Broman's teaching |
Complex Trait Community meeting, San Diego, CA (June 9, 2019)
https://github.com/kbroman/Teaching_CTC2019
Jupyter notebook:
RStudio:
ICRISAT, Patancheru, Andhra Pradesh, India (Dec 3-7, 2018)
https://github.com/kbroman/icrisat2018
Reproducible Research Workshop, Summer Institute in Statistics for Big Data, Seattle, WA (17-19 July 2017)
Reproducible Research Workshop, Summer Institute in Statistics for Big Data, Seattle, WA (16-18 July 2018)
R/qtl and R/qtl2 workshop, Complex Trait Community meeting, Memphis, TN (13 June 2017)
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
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)
- 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
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)
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]
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 ]
(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)
QTL mapping in MAGIC populations with
R/qtl2
-
Steps toward reproducible research
-
Exploratory data analysis
Statistical Consulting course, Department of Statistics, UW–Madison
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
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) ]
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)
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)]
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)
- 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
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)]