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Workshop Series: Quantitative Methods for HIV Researchers

Quantitative Methods for HIV/AIDS Research Workshop Series: Analyzing Assay Data

These workshops will explain how data is generated from the target platform, processing of the raw data, and downstream analysis and visualization. For this series, you can register for individual workshops. However, workshop 1 is mandatory for anyone registering for workshops 2, and 3 as the foundations of sequence analysis will not be reviewed.
If you would like to attend, please email kelly.sune@duke.edu directly.

Register here!

Note: The workshops are free and open to everyone but CFAR members will be given priority if we run into space constraints. Some workshops require familiarity with the R programming language to benefit.

 

1. Intro to HTS/RNA-Seq (1/16/2020)

In the Intro to HTS/RNA-Seq session we will cover: 
1. Theory of High-Throughput Sequencing and RNA-Seq 
2. Bash (UNIX command-line) and the Jupyter computing environment 
3. Analysis of RNA-Seq data from raw sequence data to read counts 
This workshop will provide background on RNA-Seq and the Jupyter computing environment necessary for the RNA-Seq Statistical Analysis session and the background on high-throughput sequencing necessary for the Microbiome Analysis session, so anyone wanting to attend those sessions are strongly encouraged to attend this one. 

This workshop does NOT assume any background besides basic understanding of molecular biology (background reading can be provided upon request for anyone not comfortable with basic molecular biology). 
 

2. Intro to Statistical Downstream Analysis of RNA-Seq Data (1/31/2020)

In this session, we will cover basic concepts, methods and tools for conducting downstream analysis of RNA-Seq data. To this end, we will review basic statistical models for count data and then carefully outline a widely used model for RNA-Seq count data. Finally, we will use R to conduct a few basic sets of analyses of pre-processed RNA-Seq count data.

This workshop assumes basic experience with R and RStudio. Anyone who did not attend Part 1 of the Quantitative Methods for HIV Researchers Workshop Series is expected to have obtained this experience elsewhere. 

 

3. Microbiome analysis (2/13/2020)

In the Microbiome Analysis session we will cover the theoretical background for high-throughput sequence microbiome analysis and hands-on bioinformatic and statistical analysis of 16S rRNA sequence data. 
This workshop assumes basic experience with R and RStudio. Anyone who did not attend Part 1 of the Quantitative Methods for HIV Researchers Workshop Series is expected to have obtained this experience elsewhere. 

 

4. Single-cell analysis (2/21/2020)

 

The workshop will focus on the concepts of multivariate single cell analysis such as cell subset identification, alignment, lineage tracing, various approaches to visualization and comparative analysis of samples. Examples will come from flow cytometry, but many of the analytic methods are also directly relevant to scRNA-seq analysis.

This workshop assumes basic experience with R and RStudio. Anyone who did not attend Part 1 of the Quantitative Methods for HIV Researchers Workshop Series is expected to have obtained this experience elsewhere. 

 

5. Analysis of antibody assays (3/6/2020) CANCELLED

 

This workshop reviews antibody binding and functional assays, and the summary statistics generated from these assays. We will consider the analysis of a single ELISA assay and additional considerations for the analysis of multiplexed platform data such as binding antibody multiplex assay (BAMA), avidity index assay (BAMA-AI) and antibody peptide microarray. We will also review the calculation of binding kinetics using SPR type approaches.

This workshop assumes basic experience with R and RStudio. Anyone who did not attend Part 1 of the Quantitative Methods for HIV Researchers Workshop Series is expected to have obtained this experience elsewhere. 

 

6. Analysis of neuro-imaging data (4/3/2020) CANCELLED

 

Imaging methods, including structural and functional MRI, diffusion tensor imaging (DTI), and positron emission tomography (PET), form an essential part of the toolbox for investigators interested in human brain function. In this workshop, participants will be introduced to the various types of imaging methods, their pros and cons, and basic analysis methods. Our focus will be on conceptual and statistical issues as opposed to particular software tools, with a view to orienting both newcomers and those whose work is not focused on neuroimaging.

 

 

Venue

Date

Day of week

Topic

Lecturer

1

Hock Auditorium

1/16/20

Thursday

Intro to HTS/RNA-Seq (and summer course experiment background)

Josh Granek

2

CRTP Classroom

1/31/20

Friday

Introduction to Statistical Downstream Analysis of RNA-Seq Data

Kouros Owzar

3

Hock Auditorium

2/13/20

Thursday

Microbiome analysis

Josh Granek

4

CRTP Classroom

2/21/20

Friday

Single-cell Analysis

John Yi

Cliburn Chan

5

CRTP Classroom

CANCELLED

Friday

Analysis of antibody assays

Stella Berendam

Cliburn Chan

6

CRTP Classroom

CANCELLED

Friday

Analysis of neuro-imaging data

John Pearson

 

Workshop sessions for each day run from 9:00-10:15, 10:15-11:45, 1:15-2:30, 2:45-4:00

Dates in Red: The CRTP classroom is not available 12-1 when we break for lunch, but we have it in the morning and afternoon.

For more information, please email kelly.sune@duke.edu