This course is part of the Genomic Data Science Specialization

Kasper Daniel Hansen, PhD

Offered By

Genomic Data Science SpecializationJohns Hopkins University

About this Course

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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.

Shareable Certificate

Earn a Certificate upon completion

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Start instantly and learn at your own schedule.

Course 6 of 8 in the

Genomic Data Science Specialization

Flexible deadlines

Reset deadlines in accordance to your schedule.

Approx. 9 hours to complete

English

Subtitles: French, Portuguese (European), 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

Genomic Data Science Specialization

Flexible deadlines

Reset deadlines in accordance to your schedule.

Approx. 9 hours to complete

English

Subtitles: French, Portuguese (European), Russian, English, Spanish

Instructor

Instructor rating

4.09/5 (13 Ratings)

Kasper Daniel Hansen, PhD

Assistant Professor, Biostatistics and Genetic Medicine

Bloomberg School of Public Health

16,264 Learners

2 Courses

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

Week

Week 1

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 Windows 3m

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

Week

Week 2

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

Biostrings7m

BSgenome6m

Biostrings - Matching6m

BSgenome - Views9m

GenomicRanges - Rle12m

GenomicRanges - Lists6m

GenomicFeatures18m

rtracklayer - Data Import14m

1 practice exercise

Quiz 230m

Week

Week 3

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

Basic Data Types4m

Annotation Overview4m

ExpressionSet Overview4m

ExpressionSet9m

SummarizedExperiment7m

GEOquery6m

biomaRt13m

R S4 Classes16m

R S4 Methods10m

1 practice exercise

Quiz 330m

Week

Week 4

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

Getting data into Bioconductor6m

Short Read4m

Rsamtools12m

oligo14m

limma16m

minfi11m

Count-based RNA-seq analysis15m

1 reading

Post Course Survey10m

1 practice exercise

Quiz 430m

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.

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, along with a variety of software implementation tools like Python, R, Bioconductor, and Galaxy. This Specialization is designed to serve as both a standalone introduction to genomic data science or as a perfect compliment to a primary degree or postdoc in biology, molecular biology, or genetics, for scientists in these fields seeking to gain familiarity in data science and statistical tools to better interact with the data in their everyday work. To audit Genomic Data Science courses for free, visit https://www.coursera.org/jhu, click the course, click Enroll, and select Audit. Please note that you will not receive a Certificate of Completion if you choose to Audit.

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.

Bioconductor for Genomic Data Science