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kbroman/Tools4RR

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Rank 279,262 (Top 6 %)
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Created about 11 years ago
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kbroman/Tools4RR

kbroman

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Materials for a one-credit course on reproducible research

Tools for Reproducible Research

Materials for a one-credit course on tools for reproducible research at UW–Madison in Spring, 2014-Spring 2016.

The website
The source for the website
The source for other material (e.g., lecture slides)

To the extent possible under law, Karl Broman has waived all copyright and related or neighboring rights to “Tools for Reproducible Research”. This work is published from the United States.

RStudioConf2019Slides

Links to slides for rstudio::conf 2019

simple_site

Minimal tutorial on making a simple website with GitHub Pages

broman

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

RStudioConf2017Slides

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

d3examples

Examples of interactive graphics using d3.js

Talk_Graphs

Talk: How to display data badly

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

miner

R package for controlling Minecraft via API

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

github_tutorial

git/github guide: Karl's minimal tutorial

steps2rr

Initial steps toward reproducible research (a minimal tutorial)

dataorg

Tutorial on organizing data in spreadsheets.

wesandersonJS

Wes Anderson palettes for javascript

knitr_knutshell

knitr in a nutshell: a brief guide to knitr

d3panels

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

minimal_make

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

hipsteR

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

Talk_OpenAccess

Slides for a talk on Open Access Publishing

Paper_DataOrg

Source for paper, "Data organization in spreadsheets"

FruitSnacks

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

Talk_ReproRes

Talk on reproducible research

JSbroman

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

conlinks

List of links to lists of links to conference slides

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

testjs

R package to test use of htmlwidgets

jhudashbike

Analysis of bike safety in Baltimore for JHU DaSH

PyBroman

Various bits of code, while I learn the language

Talk_DataCleaning

Slides for a talk on data cleaning principles

miner_book

A bookdown book on R and Minecraft

Paper_SampleMixups

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

simcross

R package to simulate and plot general experimental crosses

blog

A blogdown-based blog

horizon

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

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

Talk_WhyRR

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

Dbroman

Random D code while I learn the language

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

Talk_RRBoston2019

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

mygmailR

Send myself emails or texts, using the gmailR package

Talk_JSM2019

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

Paper_Rqtlcharts

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

Talk_DataCleaning2023

Slides for a talk on data cleaning principles

Talk_SocialMedia

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

icrisat2018

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

BMI883

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

ricalc

Genotype probability calculations for multiple-strain recombinant inbred lines

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

Talk_JSM2015

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

preCCProbPaper

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

geesibsor

Odds ratio for siblings by GEE

BMI884

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

PBPG957_Sp2018

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

Talk_DataMishap

slides for 5 min talk about a data mishap

Talk_UCSF2018

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

BMI884_spring2021

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

MUGAarrays

Reconstruct annotation files for the MegaMUGA and GigaMUGA arrays

Talk_UseR2016

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

labstat

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

testhtmlpage

Test displaying html page for a Rmd document

datacarpentry_R_2018-01-08

Data Carpentry R lessons on ecology

cubism_test

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

BMI882_spring2023

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

Recipe_cinnamon_rolls

Recipe for 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

BMI881_fall2022

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

Talk_CTC2018

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

datacarpentry_R_2016-08-23

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

npem

Analysis of cell proliferation assays

Talk_InteractiveGraphs4

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

Talk_BDSVisitDay2018

Slides for prospective Biomedical Data Science students for Visit Day 2018

Talk_GenericHMM

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

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_letter_template

Latex template for letters with UW-Madison letterhead

Talk_Purdue2018

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

Talk_BioVis

Talk for BioVis conference in Boston, July 2014

MadisonBusSchedules

Simple web app to view Madison bus schedules

CoxMapV3

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

Talk_TransHotspots

Talk on dissection and fine-mapping of trans-eQTL hotspots

Paper_MBmixups

Source files for a paper about identifiying sample mix-ups and mixtures in microbiome data

testsysfile

A throw-away R package for testing some stuff