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 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: 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: 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: 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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| Access to course materials | Available |
| Access to graded materials | Available |
| Receive a final grade | Available |
| Earn a shareable Course Certificate | Available |
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