Quantitative Methods for HIV Researchers: Workshop Series

HIV/AIDS research is generating increasingly large and complex data sets. To analyze these data sets, we need the next generation of HIV/AIDS researchers to learn skills in data processing and statistical analysis, as well as increase collaboration with quantitative scientists such as statisticians, mathematicians, computer scientists and engineers. The curriculum will train HIV/AIDS researchers in the data science and statistics skills required to analyze multi-parameter data through a series of hands-on workshops

2024 – 2025 Workshop Series: Quantitative Methods for HIV Researchers

Registration is open for Part I: Data Science Workshops. Register using this link by Tuesday, October 3, 2024.

Overview

The Quantitative Methods for HIV/AIDS workshop series is designed to provide HIV researchers with a hands-on introduction to quantitative analyses both through simple and large, complex data sets. These NIH-funded workshops are open to graduate students, postdocs, medical fellows, staff, and faculty working in the HIV/AIDS field. Non-Duke-affiliated applicants are welcome.

Details

Each part of the series consists of six once-a-week workshops held on Mondays from 1 – 4 PM. The seminars will be at Hock Plaza, and participants are encouraged to attend in person to get the most benefit. Those unable to attend in person have the option to attend virtually. Enrollment is capped at 24 participants, and participants who enroll after the cap is met will be added to a waitlist.

  • Part I workshops will teach reproducible research and R language skills along with an introduction to data analysis and study design. The seminars will be taught using RStudio. (Note: R knowledge is necessary for Part II- Statistics Workshops and Part III- Assay Analysis Workshops).
    • There will be a Day 0: Introduction to R seminar for those with no prior experience in R. Participants with R experience may skip this session, but are welcome to attend.
  • Part II workshops will build on the statistical concepts discussed in Part 1 and the utilization of predictive models using previously published HIV data. We will discuss power, type I error, hypothesis testing, linear and logistic regression, and predictive modeling.  
  • Part III workshops will teach bioinformatics skills for analysis of high throughput sequencing datasets.

NOTE: The material presented in Part I is a pre-requisite for Part II and Part III. Participants fluent with R, RStudio, and Git may skip the Part I Workshops, but must understand that the material covered in Part I will not be reviewed in Part II and Part III. Part I seminars will be recorded for attendees unable to attend Part I but interested in Parts II/III. Priority registration will be given to those who attended the previous parts.

Registration
Register by Tuesday, October 3rd.       REGISTER HERE

2024 – 2025 Workshops Schedule

PART I: Data Science Workshops (must commit to attend all 6 sessions)

Monday, Oct 7 Introduction to R (not required) Overview of general usage of R Link to Workshop Recording
Monday, Oct 21 Intro to Data Driven Research, Part 1 Discussion of Reproducible Research  
Monday, Oct 28 Intro to Data Driven Research, Part 2 The use of Tidyr and dplyr  
Monday, Nov 4 Exploratory analysis and visualization, Part 1 Visualizations with Base R and ggplot2 graphics  
Monday, Nov 11 Exploratory analysis and visualization, Part 2 The Scientific Process, common data types, calculating summary statistics and graphical summaries  
Monday, Nov 18 Exploratory analysis and visualization, Part 3 Probability Distributions. Sampling and QQ plots. Confidence intervals  
Monday, Nov 25 Case Study Walk-through Case Study walkthrough  

 

PART II: Statistical Thinking Workshops (must commit to attend all 6 sessions)

Monday, Jan 20, 2025 Hypotheses, non-parametric tests, power, and error
Monday, Jan 27, 2025 Linear regression, categorical predictors, interaction effect
Monday, Feb 3, 2025 Logistic regression and classification models
Monday, Feb 10, 2025 Random Forest and Penalized Regression
Monday, Feb 17, 2025 High-dimensional predictive models, cross-validation
Monday, Feb 24, 2025 Case Study Walk-through

 

PART III: Bioinformatics Workshops (must commit to attend all 6 sessions)

March/April 2025 TBD Tentative Topics include:

Introduction to High-throughput sequencing
Bioinformatics for RNA-seq
Statistical Analysis for RNA-seq
Bioinformatics for scRNA-seq
Pseudo-bulking, reference mapping, cluster annotation, and visualization
Differential Gene expression

 

Part I:  Data Science Workshops (must commit to attend all 6)

Day 1 Intro to Data Driven Research, Part 1 Monday, Oct 9 1 - 4 PM 214 Hock Plaza YouTube
Day 2 Intro to Data Driven Research, Part 2 Monday, Oct 23 1 - 4 PM 214 Hock Plaza YouTube
Day 3 Exploratory analysis and visualization, Part 1 Monday, Oct 30 1 - 4 PM 214 Hock Plaza YouTube
Day 4 Exploratory analysis and visualization, Part 2 Monday, Nov 6 1 - 4 PM 214 Hock Plaza YouTube
Day 5 Exploratory analysis and visualization, Part 3 Monday, Nov 13 1 - 4 PM 214 Hock Plaza YouTube
Day 6 Hands on practice: option for Bring your own data or hands on case study analysis. Monday, Nov 20 1 - 4 PM 214 Hock Plaza YouTube

 

Part II:  Statistics Workshops (must commit to attend all 6)

Day 1 Breakdown of an Experiment Monday, Jan 22 1 - 4 PM 214 Hock Plaza YouTube
Day 2 Probability, Distributions, and Confidence Intervals Monday, Jan 29 1 - 4 PM 214 Hock Plaza YouTube
Day 3 Hypothesis Testing and Power/Sample Size Monday, Feb 5 1 - 4 PM 214 Hock Plaza  
Day 4 Linear regression, categorical predictors, interaction effect Monday, Feb 12 1 - 4 PM 214 Hock Plaza YouTube
Day 5 Logistic regression and classification models Monday, Feb 19 1 - 4 PM 214 Hock Plaza YouTube
Day 6 High-dimensional predictive models, cross-validation Monday, Feb 26 1 - 4 PM 214 Hock Plaza YouTube

 

Part III: Assays Workshops

Day 1 Introduction to HTS Monday, Mar 4 1 - 4 PM 214 Hock Plaza YouTube
Day 2 Bioinformatics for RNA-seq Monday, Mar 11 1 - 4 PM 214 Hock Plaza YouTube
Day 3 Statistical Analysis for RNA-seq Monday, Mar 18 1 - 4 PM 214 Hock Plaza YouTube
Day 4 Background for scRNA-seq Monday, Mar 25 1 - 4 PM 214 Hock Plaza YouTube
Day 5 scRNA-Seq: Overview of tools; Using Seurat for QC, Transformations, and Normalization Monday, Apr 1 1 - 4 PM 214 Hock Plaza YouTube
Day 6 scRNA-Seq: Dimension reduction, Clustering, Cluster Annotation, and Visualization Monday, Apr 8 1 - 4 PM 214 Hock Plaza YouTube

PART I: Data Science Workshops (must commit to attend all 6 sessions)

Thursday, September 29 Reproducible Analysis Video
Thursday, October 6 RStudio and Base R Video
Thursday, October 20 Packages and Libraries/Intro to tidyverse Video
Thursday, October 27 Data Manipulation and Visualization with tidyverse Video
Thursday, November 3 HIV examples Video
Thursday, November 10 More examples or Bring Your Own Data Not Recorded

 

Part II: Statistics Workshops (must commit to attend all 6 sessions)
Will be held in Hock Plaza from 9am - noon

1/19/2023 Breakdown of an Experiment Video
1/26/2023 Probability, Distributions, and Confidence Intervals Video
2/2/2023 Hypothesis Testing and Power/Sample Size Video
2/9/2023 Paired and Categorical Data Approaches Video
2/16/2023 Regression, Survival, and Longitudinal Models Video
2/23/2023 Bring Your Own Project / High-level Consulting Not Recorded

 

Part III: Assays Workshops (sign up for one or more)
Will be held in Hock Plaza from 1PM - 4PM. Registration will open January 2023

3/2/2023 Introduction to High-throughput sequencing
3/9/2023 Bioinformatics for RNA-seq
3/16/2023 Statistical Analysis for RNA-seq
3/23/2023 Microbiome analysis
3/30/2023 Bioinformatics for Flow cytometry
4/6/2023 Bioinformatics for ScRNA-seq