OpenMendel Workshop @ ASHG Annual Meeting 2020

This repo contains the OpenMendel tutorials presented in the workshop at the ASHG Annual Meeting on Oct 27-30, 2020.

Presenters

Professors Kenneth Lange (UCLA), Janet Sinsheimer (UCLA), Eric Sobel (UCLA), Jin Zhou (University of Arizona), Hua Zhou (UCLA), and doctoral students.

How to run tutorials?

There are two ways to run the Jupyter notebook tutorials.

1. To run the Jupyter notebooks in cloud, click the Binder icon
   
   and navigate to the Jupyter notebooks ipynb in each subfolder. Or click the Binder link below for each individual tutorial directly.

2. To run Jupyter notebooks on your own machine, (1) first git clone https://github.com/OpenMendel/ASHG-OpenMendelWorkshop-2020-Oct.git to sync the most recent course materials to your computer, (2) install all needed Julia packages by using Pkg; Pkg.instantiate(), (3) open individual notebook by Using IJulia; notebook("pathtoipynb").

What is OpenMendel

• Mendel: comprehensive genetic analysis software by Ken Lange, Eric Sobel, Janet Sinsheimer, and Hua Zhou.

• Julia: Walk Like Python; Run Like C.

• Ken's vision: Julia + Mendel = OpenMendel.

How to contribute?

• Browse existing OpenMendel packages: https://github.com/OpenMendel. Don't forget to star them 😄

• Ask questions, file bug reports, and request new features by GitHub Issues.

• Get credit for your code contribution via GitHub Fork and Pull Requests.

• Want project ideas? Talk to any of us or come to OpenMendel Zoom meetings (every Wed).

Syllabus

Time	Topic	Presenter	Slides
4 min	Overview of OpenMendel project	Kenneth Lange	[pdf]
4 min	Using OpenMendel on biobank data	Jin Zhou	[pdf]
4 min	Jupyter Notebooks	Janet Sinsheimer	[pdf]
10 min	Import genotype data by SnpArrays.jl [Binder] [ipynb] [html]	Hua Zhou	[pdf]
10 min	Variance component models [Binder] [ipynb] [html]	Juhyun Kim	[pdf]
10 min	GWAS for ordinal traits [Binder] [ipynb] [html]	Chris German	[pdf]
10 min	Genotype imputation and phasing [Binder] [ipynb][html]	Ben Chu	[pdf]
4 min	Ongoing work	Xinkai Zhou	[pdf]
4 min	Contribute to OpenMendel	Eric Sobel	[pdf]