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 |