Bioconductor for Genomic Data Science

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Bioconductor for Genomic Data Science

Coursera (CC)
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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 3.9 stars Average User Rating 3.9See what learners said Coursework

Each course is like an interactive textbook, f…

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When you enroll for courses through Coursera you get to choose for a paid plan or for a free plan

  • Free plan: No certicification and/or audit only. You will have access to all course materials except graded items.
  • Paid plan: Commit to earning a Certificate—it's a trusted, shareable way to showcase your new skills.

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 3.9 stars Average User Rating 3.9See what learners said Coursework

Each course is like an interactive textbook, featuring pre-recorded videos, quizzes and projects.

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Johns Hopkins University The mission of The Johns Hopkins University is to educate its students and cultivate their capacity for life-long learning, to foster independent and original research, and to bring the benefits of discovery to the world.

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 expand


  1. Reading: Welcome
  2. Reading: Syllabus
  3. Reading: Pre Course Survey
  4. Video: Installing R on Windows
  5. Video: Installing R on A Mac
  6. Video: Installing R Studio on a Mac
  7. Video: What is Bioconductor
  8. Video: Installing Bioconductor
  9. Video: The Bioconductor Website
  10. Video: Useful Online Resources
  11. Video: R Base Types
  12. Video: GRanges - Overview
  13. Video: IRanges - Basic Usage
  14. Video: GenomicRanges - GRanges
  15. Video: GenomicRanges - Basic GRanges Usage
  16. Video: GenomicRanges - seqinfo
  17. Video: AnnotationHub
  18. Video: Usecase: AnnotationHub and GRanges, part 1
  19. 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 expand


  1. Video: Biostrings
  2. Video: BSgenome
  3. Video: Biostrings - Matching
  4. Video: BSgenome - Views
  5. Video: GenomicRanges - Rle
  6. Video: GenomicRanges - Lists
  7. Video: GenomicFeatures
  8. 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 expand


  1. Video: Basic Data Types
  2. Video: Annotation Overview
  3. Video: ExpressionSet Overview
  4. Video: ExpressionSet
  5. Video: SummarizedExperiment
  6. Video: GEOquery
  7. Video: biomaRt
  8. Video: R S4 Classes
  9. 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 expand


  1. Video: Getting data into Bioconductor
  2. Video: Short Read
  3. Video: Rsamtools
  4. Video: oligo
  5. Video: limma
  6. Video: minfi
  7. Video: Count-based RNA-seq analysis
  8. Reading: Post Course Survey

Graded: Quiz 4
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