About this course: In this culminating project, you will deploy the tools and techniques that you've mastered over the course of the specialization. You'll work with a real data set to perform analyses and prepare a report of your findings.
Created by: Johns Hopkins University
Taught by: Jeff Leek, PhD, Associate Professor, Biostatistics
Bloomberg School of Public Health
Taught by: Kasper Daniel Hansen, PhD, Assistant Professor, Biostatistics and Genetic Medicine
Bloomberg School of Public Health
| Basic Info | Course 8 of 8 in the Genomic Data Science Specialization |
| Commitment | 8 weeks of study, 2-4 hours/week |
| Language | English |
| How To Pass | Pass all graded assignments to complete the course. |
| User Ratings |
Syllabus
WEEK 1
Introduction
In this first week, we'll introduce the project and get you oriented to the tasks that you'll be performing over the next several weeks.
1 video, 6 readings
- Video: Introduction to the Capstone - Kasper Hansen
- Reading: Welcome
- Reading: The big question
- Reading: What you will be doing in this capstone project
- Reading: Passing the Capstone
- Reading: Why re-analysis?
- Reading: Why is this so hard?
WEEK 2
Introduction to the Dataset - Andrew Jaffe
This week, we'll really dig into the dataset by providing an introduction from Andrew Jaffe, the lead scientist on the analysis. You should also be looking ahead to Task 2, which is due in Week 4; the alignment will take a long time to perform, so you should start early.
1 video, 3 readings
- Video: The Dataset - Andrew Jaffe
- Reading: Phenotype information
- Reading: Getting the data from SRA
- Reading: Which samples to use
WEEK 3
Understand the Problem
The purpose of genomic data science is to answer fundamental questions in biology. Before starting on the data analysis process, the first step is always to understand the scientific question you are trying to answer. Don't forget to stay on top of the alignment task due in Week 4; it will take a long time to accomplish and shouldn't be put off.
1 video, 1 reading
- Reading: Task 1 Instructions
- Video: The Results - Andrew Jaffe
- Discussion Prompt: What did you find challenging about task 1?
Graded: Understand the problem
WEEK 4
Alignment
Once you have understood the problem, the next step is to obtain the raw data so that you can perform your analysis.
2 items
- Discussion Prompt: What did you find challenging about task 2?
Graded: Alignment
WEEK 5
QC the Alignment
Now you have aligned the data, the next step is to do some quality control to make sure that the data are in good shape.
2 items
- Discussion Prompt: What did you find challenging about task 3?
Graded: QC the Alignment
WEEK 6
Get Feature Counts
Now that you have performed alignment and quality control, the next step is to calculate the abundance of every gene in every sample.
2 items
- Discussion Prompt: What did you find challenging about task 4?
Graded: Get Feature Counts
WEEK 7
Exploratory Analysis
After summarizing your genomic data the next step is to load the data into R for analysis with Bioconductor.
2 items
- Discussion Prompt: What did you find challenging about task 5?
Graded: Exploratory Analysis
WEEK 8
Statistical Analysis
The next step is to perform a statistical analysis to detect genes that are differentially expressed.
2 items
- Discussion Prompt: What did you find challenging about task 6?
Graded: Statistical Analysis
WEEK 9
Gene Set Analysis
In task 6, we have identified genes differentially expressed between fetal and adult brain. Now we will examine these results in a wider context.
3 items
- Discussion Prompt: What did you find challenging about task 7?
- Peer Review: Optional Peer Review of Your Report Draft
Graded: Gene Set Analysis
WEEK 10
Describe Your Analysis
The next step is to document your work. One of the major issues in genomic data science is that there are so many steps in the process. If these steps are not documented well the result can be major problems.
2 items
- Discussion Prompt: What did you find challenging about task 8?
Graded: Describe Your Analysis
FAQs
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Pricing
| Audit | Purchase Course | |
|---|---|---|
| Access to course materials | Available | Available |
| Access to graded materials | Not available | Available |
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Ratings and Reviews
Really practical project in the genomics field!
Excellent set of assignments to apply multiple tools used in the specialization!
Very much helpful course. I appreciate it.
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Quite time demanding when genomics is not your primary field, but I have learnt so much!