Discover kbroman/miner_book Open Source project

R/broman: A package with Karl Broman's personal R code

179

broman

175

RStudioConf2017Slides

Links to slides for talks at the 2017 rstudio::conf

141

d3examples

Examples of interactive graphics using d3.js

Materials for a one-credit course on reproducible research

130

Tools4RR

Talk: How to display data badly

129

Talk_Graphs

datasciquotes

Data Science related quotes

pkg_primer

R package primer: a minimal tutorial on writing R packages

qtlcharts

R/qtlcharts: An R package for interactive QTL graphics

R package for controlling Minecraft via API

miner

JSM2016slides

Links to slides for talks at the 2016 Joint Statistical Meetings in Chicago

OpenVisConf2017Slides

Links to slides from OpenVisConf 2017

qtl

R/qtl: A QTL mapping environment

ProgrammingNotes

My personal notes on various programming languages and tools

kbroman.github.io

Karl Broman's website

git/github guide: Karl's minimal tutorial

github_tutorial

Initial steps toward reproducible research (a minimal tutorial)

steps2rr

Tutorial on organizing data in spreadsheets.

dataorg

Wes Anderson palettes for javascript

wesandersonJS

CSS

knitr_knutshell

knitr in a nutshell: a brief guide to knitr

A library of d3-based graphic panels, written in CoffeeScript

d3panels

Minimal make: A minimal tutorial on the most important tool for reproducible research

minimal_make

A tutorial to re-educate people with learned R before it was cool

hipsteR

Slides for a talk on Open Access Publishing

Talk_OpenAccess

Source for paper, "Data organization in spreadsheets"

Paper_DataOrg

Counts of each type of fruit snack in each package in a box of 80 packages.

FruitSnacks

Talk_ReproRes

Talk on reproducible research

Bits of JavaScript and CoffeeScript code, as I learn the languages (with a focus on interactive graphics)

JSbroman

List of links to lists of links to conference slides

conlinks

craft

Extra functions to be used with the miner package

lmmlite

Simple port of pylmm: linear mixed models for GWAS

academics.wtf

website academics.wtf

R package to test use of htmlwidgets

testjs

CSS

jhudashbike

Analysis of bike safety in Baltimore for JHU DaSH

Various bits of code, while I learn the language

PyBroman

Python

Talk_DataCleaning

Slides for a talk on data cleaning principles

Source for paper, "Identification and correction of sample mix-ups in expression genetic data: A case study"

Paper_SampleMixups

R package to simulate and plot general experimental crosses

simcross

blog

A blogdown-based blog

R package to make a static horizon chart with cubism.js

horizon

JavaScript

Poster_SampleMixups

Poster on Identifying and correcting sample mix-ups in eQTL data

qtlbook

R/qtlbook: Datasets for the R/qtl book

RR_Workshop

Materials for a 1-hour workshop on reproducible research

Python

Talk_WhyRR

Slides for a short introduction, on "Why reproducible research"

Random D code while I learn the language

Dbroman

xoi

R/xoi: Tools for analyzing crossover interference

crayonsJS

Crayon colors for JavaScript

lineup

R/lineup package to detect sample mix-ups between two sets of measurements

PearsonData

Data extracted from Pearson and Lee (1903) On the Laws of Inheritance in Man: I. Inheritance of Physical Characters

phyloQTLpaper

Source for the paper Broman et al. (2012) Mapping quantitative trait loci onto a phylogenetic tree. Genetics 192:267-279

PostScript

Talk_RRBoston2019

Slides for a talk for a reproducible research workshop at Boston University on 2019-05-14

Send myself emails or texts, using the gmailR package

mygmailR

Talk_JSM2019

Slides for very short presentation as part of panel on Javascript at JSM 2019

Source for paper, R/qtlcharts: interactive graphics for quantitative trait locus mapping

Paper_Rqtlcharts

JavaScript

Talk_DataCleaning2023

Slides for a talk on data cleaning principles

Slides for a talk on "Social media for data scientists"

Talk_SocialMedia

Materials for a workshop on advanced R and R/qtl, ICRISAT, Hyderabad, India, 3-7 Dec 2018

icrisat2018

Web site for BMI 883 course on "Biomedical data science professional skills"

BMI883

Genotype probability calculations for multiple-strain recombinant inbred lines

ricalc

ailProbPaper

Source for the paper Broman KW (2012) Haplotype probabilities in advanced intercross populations. G3 2:199-202

mbmixture

R package for evaluating a microbiome sample as a potential mixture

Poster_ENAR2014

Poster: Data visualizations should be more interactive, for ENAR 2014

Slides for a talk on interactive graphs, for Joint Statistical Meetings in Seattle, 10 Aug 2015

Talk_JSM2015

Source for paper Broman KW (2012) Genotype probabilities at intermediate generations in the construction of recombinant inbred lines. Genetics 190:403-412

preCCProbPaper

PostScript

geesibsor

Odds ratio for siblings by GEE

BMI884

Web site for BMI 884 course on "Biomedical data science professional skills"

Materials for spring, 2018, seminar course in Plant Breeding at UW-Madison

PBPG957_Sp2018

Talk_DataMishap

slides for 5 min talk about a data mishap

Slides for a seminar at UC-San Francisco on 1 Feb 2018

Talk_UCSF2018

BMI884_spring2021

BMI 884 (Biomedical data science professional skills 2) from Spring, 2021

Reconstruct annotation files for the MegaMUGA and GigaMUGA arrays

MUGAarrays

Slides for a talk on "R/qtl: Just barely sustainable" for UseR 2016 at Stanford, 28 June 2016

Talk_UseR2016

R package with datasets used in an old course on Statistics for Laboratory Scientists

labstat

testhtmlpage

Test displaying html page for a Rmd document

Data Carpentry R lessons on ecology

datacarpentry_R_2018-01-08

Trying to figure out how to use cubism.js with static data

cubism_test

JavaScript

BMI882_spring2023

BMI 882 (Biomedical data science scholarly literature 2) from Spring, 2023

Recipe for cinnamon rolls

Recipe_cinnamon_rolls

Talk_Rqtl2_CTC2017

Slides for a talk on "R/qtl2: high-dimensional data and multi-parent populations" for CTC 2017

Talk_SampleMixups

Slides for a talk on identifying and correcting sample mix-ups in high-dimensional genetic data

fingers

Identifying clusters of related individuals

Teaching_UWStatGen2019

QTL mapping lectures for Stat 877 (Stat methods for molecular biology) for Spring, 2019

BMI 881 (Biomedical data science scholarly literature 1) from Fall, 2022

BMI881_fall2022

Slides for a talk at the Complex Trait Community meeting in Glasgow in June, 2018

Talk_CTC2018

datacarpentry_R_2016-08-23

Data Carpentry R lessons on ecology http://datacarpentry.github.io/R-ecology-lesson

Analysis of cell proliferation assays

npem

Talk_InteractiveGraphs4

Slides for a talk on interactive graphs, for Harvard Biostat 2014-11-06

Slides for prospective Biomedical Data Science students for Visit Day 2018

Talk_BDSVisitDay2018

Slides for a talk on a generic HMM for multi-parent populations (for CTC 2021)

Talk_GenericHMM

Teaching_UWStatGen2022

Lecture on QTL mapping in multi-parent populations, for BMI/Stat 877 at UW-Madison

BMI881

Web site for BMI 881 course on "Biomedical data science scholarly literature"

Latex template for letters with UW-Madison letterhead

latex_letter_template

Slides for a talk at Purdue Symposium on Statistics, 7 June 2018

Talk_Purdue2018

Talk_BioVis

Talk for BioVis conference in Boston, July 2014

Simple web app to view Madison bus schedules

MadisonBusSchedules

Revised Cox et al. mouse genetic map, for build 39 of the mouse genome

CoxMapV3