Teaching and Resources

Recently Taught Courses

SISG 2025 - Gene Regulation Moduls: TWAS, ChiP-seq Analysis, Functional Noncoding Variants

1. Introduction to TWAS
2. TWAS with Summary xQTL Data and Finemapping
3. TWAS and Mendelian Randomization
4. ChiP-seq Analysis Pipeline
5. Analysis with Functions of Noncoding Variants

BIOS-770 - Advanced Statistical Genetics: GWAS

1. Genotype Imputation, Single Variant GWAS
2. QC, Population Stratification, LMM
3. Finemap, Bayesian Functional GWAS
4. Rare Variant Test, Pleiotropy, Mendelian Randomization

IBS-519 - Data Analysis using R

1. Linear Regression
2. ANOVA
3. Power Analysis
4. Permutation Test
5. Introductions to Machine Learning

IBS-538 - Data Science

1. Multivariate Analysis with Application to RNAseq Differential Gene Expression Analysis

High Performance and Cloud Computing Cluster

HGCC

• Introductions to New HGCC
• Run Computation Tools and Submit Jobs on HGCC
  • Slurm User Guide from University of Michigan
• Introductions to BASH.
  • Bash Scripting Tutorial

RHPC

• Introductions to RHPC
• RSPH High Performance Computing Github : Starting guides are provided.
• Helpful tips from Dr. Hao Wu

HyPER-C3

• Start Guide for using HyPER-C3 HPC

Emory Amazon Web Service (AWS)

• Introductions to Emory AWS
• AWS Documentation

Other Resources

Bioinformatics

1. Bioinformatics workshop documentations by UCDAVIS Bioinformatics Core with the following Covered Topics:
   • Bioinformatics Prerequisites (Command Line and R)
   • Single-Cell RNA-Seq Analysis
   • RNA-seq Analysis
   • Microbial Community Analysis (Amplicon)
   • Variant Analysis (Variant calling with GATK, Variant Annotation)

2. Analysis of single cell RNA-seq data by Hemberg lab, Welcome Sanger Institute, UK

3. ENAR 2021 short course on single cell RNA-seq analysis by Hao Wu, Emory University, and Ziyi Li, MD Anderson Cancer Center

4. Bioinformatics Training at the Harvard Chan Bioinformatics Core

Linux

• Beginner’s Guide for Linux (long version)

  • bash-scripting-tutorial-linux-shell-script-and-command-line-for-beginners (short version)

  • Essential Linux Commands

  • Tutorial of AWK: AWK is a powerful tool for handling large text files in Linux system.

  • Tmux Cheat Sheet: Tmux is a useful tool to split terminal screens.

  • Learn VIM : Vim is a useful text editor tool in Linux.

• Visual Studio Code is recommend for connecting to clusters and editing scripts on clusters.
  • YouTub Instructions about Connecting VS Code to HPC
  • VS Code Instructions by NYU

• Get started with GitHub : GitHub is a cloud-based platform where you can store, share, and work together with others to write code.

• Cheat Sheets of AWK, C++, Python, R, Vim, Git, etc.

R

• R/Rstudio Tutorial Essential Videos

Coursera Python Courses

• Programming for Everybody (Getting Started with Python)
• Applied Data Science with Python

Jupyter Notebook (Recommended for Programing with Python)

• Introduction to Jupyter Notebooks
• Jupyter Kernels

Scientific Writing and Presentations

Scientific Writing

• Write ASHG Abstract
• Ten simple rules for structuring papers. PLOS Computational Biology, 2017.
• Ten simple rules for writing a response to reviewers. PLOS Computational Biology, 2017.
  • Example peer review process for PLOS Genetics with reviewers’ comments and response letters.
• Me write pretty one day: how to write a good scientific paper. Journal of Cell Biology, 2004.

Scientific Presentations

Poster Presentations

• How to Make An Effective Poster

Oral Scientific Presentations

• Scientific Presetnations 101
• Structure of a 10-minute Oral Scientific Presentation
• The Art of Great Talks