Bioconductor for Genomic Data Science
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Bioconductor for Genomic Data Science
This course is part of Genomic Data Science Specialization
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There are 4 modules in 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.
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.
What's included
16 videos3 readings1 assignment
16 videos•Total 126 minutes
- Installing R on Windows •3 minutes
- Installing R on A Mac •2 minutes
- Installing R Studio on a Mac •2 minutes
- What is Bioconductor•7 minutes
- Installing Bioconductor•4 minutes
- The Bioconductor Website•10 minutes
- Useful Online Resources•5 minutes
- R Base Types•18 minutes
- GRanges - Overview•5 minutes
- IRanges - Basic Usage•12 minutes
- GenomicRanges - GRanges•9 minutes
- GenomicRanges - Basic GRanges Usage•8 minutes
- GenomicRanges - seqinfo•6 minutes
- AnnotationHub•8 minutes
- Usecase: AnnotationHub and GRanges, part 1•13 minutes
- Usecase: AnnotationHub and GRanges, part 2•14 minutes
3 readings•Total 30 minutes
- Welcome•10 minutes
- Syllabus•10 minutes
- Pre Course Survey•10 minutes
1 assignment•Total 30 minutes
- Quiz 1•30 minutes
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.
What's included
8 videos1 assignment
8 videos•Total 81 minutes
- Biostrings•7 minutes
- BSgenome•7 minutes
- Biostrings - Matching•6 minutes
- BSgenome - Views•9 minutes
- GenomicRanges - Rle•12 minutes
- GenomicRanges - Lists•6 minutes
- GenomicFeatures•19 minutes
- rtracklayer - Data Import•15 minutes
1 assignment•Total 30 minutes
- Quiz 2•30 minutes
In this week we will cover Basic Data Types, ExpressionSet, biomaRt, and R S4.
What's included
9 videos1 assignment
9 videos•Total 79 minutes
- Basic Data Types•5 minutes
- Annotation Overview•5 minutes
- ExpressionSet Overview•4 minutes
- ExpressionSet•10 minutes
- SummarizedExperiment•8 minutes
- GEOquery•7 minutes
- biomaRt•14 minutes
- R S4 Classes•17 minutes
- R S4 Methods•10 minutes
1 assignment•Total 30 minutes
- Quiz 3•30 minutes
In this week, we will cover Getting data in Bioconductor, Rsamtools, oligo, limma, and minfi
What's included
7 videos1 reading1 assignment
7 videos•Total 81 minutes
- Getting data into Bioconductor•7 minutes
- Short Read•4 minutes
- Rsamtools•13 minutes
- oligo•14 minutes
- limma•17 minutes
- minfi•11 minutes
- Count-based RNA-seq analysis•16 minutes
1 reading•Total 10 minutes
- Post Course Survey•10 minutes
1 assignment•Total 30 minutes
- Quiz 4•30 minutes
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Johns Hopkins University
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Johns Hopkins University
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Johns Hopkins University
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Johns Hopkins University
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Reviewed on May 20, 2018
It's very helpful in learning genomic data science. I think it's a little difficult in the beginning. The instructor have some accent, which made me even harder to get into it.
Reviewed on Sep 3, 2016
A nice course to introduce Bioconductor to students
Reviewed on Mar 11, 2016
Excellent introduction to Bioconductor. Thanks to the team. However, absence of inputs from TA or Instructor was felt in the discussion.
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