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 |