About this course: Learn to use tools from the Bioconductor project to perform analysis of genomic data. This is the fifth course in the Genomic Big Data Specialization from Johns Hopkins University.
Created by: Johns Hopkins University
Taught by: Kasper Daniel Hansen, PhD, Assistant Professor, Biostatistics and Genetic Medicine
Bloomberg School of Public Health
| Basic Info | Course 6 of 8 in the Genomic Data Science Specialization |
| Language | English |
| How To Pass | Pass all graded assignments to complete the course. |
| User Ratings |
Syllabus
WEEK 1
Week One
The class will cover how to install and use Bioconductor software. We will discuss common data structures, including ExpressionSets, SummarizedExperiment and GRanges used across several types of analyses.
16 videos, 3 readings
- Reading: Welcome
- Reading: Syllabus
- Reading: Pre Course Survey
- Video: Installing R on Windows
- Video: Installing R on A Mac
- Video: Installing R Studio on a Mac
- Video: What is Bioconductor
- Video: Installing Bioconductor
- Video: The Bioconductor Website
- Video: Useful Online Resources
- Video: R Base Types
- Video: GRanges - Overview
- Video: IRanges - Basic Usage
- Video: GenomicRanges - GRanges
- Video: GenomicRanges - Basic GRanges Usage
- Video: GenomicRanges - seqinfo
- Video: AnnotationHub
- Video: Usecase: AnnotationHub and GRanges, part 1
- Video: Usecase: AnnotationHub and GRanges, part 2
Graded: Quiz 1
WEEK 2
Week Two
In this week we will learn how to represent and compute on biological sequences, both at the whole-genome level and at the level of millions of short reads.
8 videos
- Video: Biostrings
- Video: BSgenome
- Video: Biostrings - Matching
- Video: BSgenome - Views
- Video: GenomicRanges - Rle
- Video: GenomicRanges - Lists
- Video: GenomicFeatures
- Video: rtracklayer - Data Import
Graded: Quiz 2
WEEK 3
Week Three
In this week we will cover Basic Data Types, ExpressionSet, biomaRt, and R S4.
9 videos
- Video: Basic Data Types
- Video: Annotation Overview
- Video: ExpressionSet Overview
- Video: ExpressionSet
- Video: SummarizedExperiment
- Video: GEOquery
- Video: biomaRt
- Video: R S4 Classes
- Video: R S4 Methods
Graded: Quiz 3
WEEK 4
Week Four
In this week, we will cover Getting data in Bioconductor, Rsamtools, oligo, limma, and minfi
7 videos, 1 reading
- Video: Getting data into Bioconductor
- Video: Short Read
- Video: Rsamtools
- Video: oligo
- Video: limma
- Video: minfi
- Video: Count-based RNA-seq analysis
- Reading: Post Course Survey
Graded: Quiz 4
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Pricing
| Audit | Purchase Course | |
|---|---|---|
| Access to course materials | Available | Available |
| Access to graded materials | Not available | Available |
| Receive a final grade | Not available | Available |
| Earn a shareable Course Certificate | Not available | Available |
Ratings and Reviews
pretty good
Lots of good data. Really a walk through of coding without too much theory. Would prefer a little more theory. Would have helped in completing the course and capstone. Ended up having to take Eric Lander Intro to Bio course on edx to really understand what I had done. In particular, a better explanation of what is going on at a basic with methylation marks and how the Epigenome Map was constructed.
It is a good start for people who study epigenomics!
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I'm going to take this again! hard one.