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

2023 -2024 Workshop Series: Quantitative Methods for HIV Researchers

Registration for the Part III: Assays Workshops is open through Monday, February 26, 2024.
Click here to register:
https://duke.qualtrics.com/jfe/form/SV_7TZZ2yDe3NBiVBs

The Quantitative Methods for HIV Researchers workshop series is designed to provide HIV researchers with the quantitative skills necessary for analysis of large, complex data sets resulting from assays such as single-cell RNA-seq, flow cytometry, fMRI, etc. These NIH-funded workshops are open to graduate students, postdocs, medical fellows, staff and faculty. Non-Duke-affiliated applicants are welcome.

The course will be taught at Hock Plaza, and it is highly recommended that you attend in person to get the most benefit. Those unable to attend in person have the option to attend virtually. The maximum number for the class is 24 – there is a waiting list when the limit is met.

The Part I workshops will teach you R language and environment skills needed for statistical computing and graphics. The R environment is an integrated suite of software facilities for data manipulation, calculation and graphical display, and knowledge of R is required for the Part II- Statistics Workshops and Part III- Assay Analysis Workshops.

In Part II of this workshop series, attendees will learn important concepts in statistics and perform statistical analyses using real HIV data. We will introduce different types of clinical research studies, perform exploratory data analysis with numerical and graphical summaries and introduce hypothesis testing, and appropriate methods for modeling different types of outcomes.

In Part III of this workshop series, attendees will learn skills for analysis of large, complex data sets resulting from assays.

2023 - 2024 Workshops Schedule

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

 

Email questions to kelly.sune@duke.edu

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