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.
This course is part of the Genomic Data Science Specialization
Bioconductor for Genomic Data Science
Offered By
Syllabus - What you will learn from this course
Week
13 hours to complete
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 (Total 126 min), 3 readings, 1 quiz
16 videos
Installing R on A Mac 2m
Installing R Studio on a Mac 1m
What is Bioconductor7m
Installing Bioconductor3m
The Bioconductor Website9m
Useful Online Resources5m
R Base Types18m
GRanges - Overview4m
IRanges - Basic Usage12m
GenomicRanges - GRanges8m
GenomicRanges - Basic GRanges Usage8m
GenomicRanges - seqinfo6m
AnnotationHub8m
Usecase: AnnotationHub and GRanges, part 112m
Usecase: AnnotationHub and GRanges, part 213m
3 readings
Welcome10m
Syllabus10m
Pre Course Survey10m
1 practice exercise
Quiz 120m
Week
22 hours to complete
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 (Total 81 min), 1 quiz
8 videos
BSgenome6m
Biostrings - Matching6m
BSgenome - Views9m
GenomicRanges - Rle12m
GenomicRanges - Lists6m
GenomicFeatures18m
rtracklayer - Data Import14m
1 practice exercise
Quiz 220m
Week
32 hours to complete
Week Three
In this week we will cover Basic Data Types, ExpressionSet, biomaRt, and R S4.
9 videos (Total 79 min), 1 quiz
9 videos
Annotation Overview4m
ExpressionSet Overview4m
ExpressionSet9m
SummarizedExperiment7m
GEOquery6m
biomaRt13m
R S4 Classes16m
R S4 Methods10m
1 practice exercise
Quiz 320m
Week
42 hours to complete
Week Four
In this week, we will cover Getting data in Bioconductor, Rsamtools, oligo, limma, and minfi
7 videos (Total 81 min), 1 reading, 1 quiz
7 videos
Short Read4m
Rsamtools12m
oligo14m
limma16m
minfi11m
Count-based RNA-seq analysis15m
1 reading
Post Course Survey10m
1 practice exercise
Quiz 420m
4.0
36 ReviewsTop Reviews
Excellent introduction to Bioconductor. Thanks to the team. However, absence of inputs from TA or Instructor was felt in the discussion.
Amazing course, motivated me to use bio conductor for descriptive seq studies of DNA.
Instructor
Kasper Daniel Hansen, PhD
Assistant Professor, Biostatistics and Genetic MedicineBloomberg School of Public Health
About 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.
About the Genomic Data Science Specialization
This specialization covers the concepts and tools to understand, analyze, and interpret data from next generation sequencing experiments. It teaches the most common tools used in genomic data science including how to use the command line, Python, R, Bioconductor, and Galaxy. The sequence is a stand alone introduction to genomic data science or a perfect compliment to a primary degree or postdoc in biology, molecular biology, or genetics.
To audit Genomic Data Science courses for free, visit https://www.coursera.org/jhu, click the course, click Enroll, and select Audit.
Frequently Asked Questions
When will I have access to the lectures and assignments?
Once you enroll for a Certificate, you’ll have access to all videos, quizzes, and programming assignments (if applicable). Peer review assignments can only be submitted and reviewed once your session has begun. If you choose to explore the course without purchasing, you may not be able to access certain assignments.
What will I get if I subscribe to this Specialization?
When you enroll in the course, you get access to all of the courses in the Specialization, and you earn a certificate when you complete the work. Your electronic Certificate will be added to your Accomplishments page - from there, you can print your Certificate or add it to your LinkedIn profile. If you only want to read and view the course content, you can audit the course for free.
What is the refund policy?
Is financial aid available?
More questions? Visit the Learner Help Center.
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