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.
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Genomic Data Science SpecializationJohns Hopkins UniversityAbout this Course
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Course 6 of 8 in the
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Approx. 9 hours to complete
English
Subtitles: French, Portuguese (Brazilian), Russian, English, Spanish
Skills you will gain
BioinformaticsBioconductorGenomicsR Programming
Shareable Certificate
Earn a Certificate upon completion
100% online
Start instantly and learn at your own schedule.
Course 6 of 8 in the
Flexible deadlines
Reset deadlines in accordance to your schedule.
Approx. 9 hours to complete
English
Subtitles: French, Portuguese (Brazilian), Russian, English, Spanish
Offered by
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 - What you will learn from this course
3 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.
3 hours to complete
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 130m
2 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.
2 hours to complete
8 videos (Total 81 min)
8 videos
BSgenome6m
Biostrings - Matching6m
BSgenome - Views9m
GenomicRanges - Rle12m
GenomicRanges - Lists6m
GenomicFeatures18m
rtracklayer - Data Import14m
1 practice exercise
Quiz 230m
2 hours to complete
Week Three
In this week we will cover Basic Data Types, ExpressionSet, biomaRt, and R S4.
2 hours to complete
9 videos (Total 79 min)
9 videos
Annotation Overview4m
ExpressionSet Overview4m
ExpressionSet9m
SummarizedExperiment7m
GEOquery6m
biomaRt13m
R S4 Classes16m
R S4 Methods10m
1 practice exercise
Quiz 330m
2 hours to complete
Week Four
In this week, we will cover Getting data in Bioconductor, Rsamtools, oligo, limma, and minfi
2 hours to complete
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 430m
Reviews
TOP REVIEWS FROM BIOCONDUCTOR FOR GENOMIC DATA SCIENCE
by JKAug 30, 2016
I think it is a good class overall but the pace is fast and the resources that can help you is lacking. This will be good for someone who already kind of understands bioconductor.
by GKAug 27, 2019
Before you can run, you must learn to walk. Kasper's well paced tutorials will give you confidence using the tools you need for genomic study.
by MAMar 11, 2016
Excellent introduction to Bioconductor. Thanks to the team. However, absence of inputs from TA or Instructor was felt in the discussion.
by ABApr 11, 2018
Amazing course, motivated me to use bio conductor for descriptive seq studies of DNA.
About the Genomic Data Science Specialization
With genomics sparks a revolution in medical discoveries, it becomes imperative to be able to better understand the genome, and be able to leverage the data and information from genomic datasets. Genomic Data Science is the field that applies statistics and data science to the genome.
Frequently Asked Questions
When will I have access to the lectures and assignments?
Access to lectures and assignments depends on your type of enrollment. If you take a course in audit mode, you will be able to see most course materials for free. To access graded assignments and to earn a Certificate, you will need to purchase the Certificate experience, during or after your audit. If you don't see the audit option:
- The course may not offer an audit option. You can try a Free Trial instead, or apply for Financial Aid.
- The course may offer 'Full Course, No Certificate' instead. This option lets you see all course materials, submit required assessments, and get a final grade. This also means that you will not be able to purchase a Certificate experience.
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.
Is financial aid available?
Yes, Coursera provides financial aid to learners who cannot afford the fee. Apply for it by clicking on the Financial Aid link beneath the "Enroll" button on the left. You'll be prompted to complete an application and will be notified if you are approved. You'll need to complete this step for each course in the Specialization, including the Capstone Project. Learn more.
More questions? Visit the Learner Help Center.
