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.
本课程是 Genomic Data Science 专项课程 专项课程的一部分
Bioconductor for Genomic Data Science
提供方
教学大纲 - 您将从这门课程中学到什么
周
1Week 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 个视频 （总计 126 分钟）, 3 个阅读材料, 1 个测验
16 个视频
Installing R on A Mac 2分钟
Installing R Studio on a Mac 1分钟
What is Bioconductor7分钟
Installing Bioconductor3分钟
The Bioconductor Website9分钟
Useful Online Resources5分钟
R Base Types18分钟
GRanges - Overview4分钟
IRanges - Basic Usage12分钟
GenomicRanges - GRanges8分钟
GenomicRanges - Basic GRanges Usage8分钟
GenomicRanges - seqinfo6分钟
AnnotationHub8分钟
Usecase: AnnotationHub and GRanges, part 112分钟
Usecase: AnnotationHub and GRanges, part 213分钟
3 个阅读材料
Welcome10分钟
Syllabus10分钟
Pre Course Survey10分钟
1 个练习
Quiz 120分钟
周
2Week 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 个视频 （总计 81 分钟）, 1 个测验
8 个视频
Biostrings7分钟
BSgenome6分钟
Biostrings - Matching6分钟
BSgenome - Views9分钟
GenomicRanges - Rle12分钟
GenomicRanges - Lists6分钟
GenomicFeatures18分钟
rtracklayer - Data Import14分钟
1 个练习
Quiz 220分钟
周
3Week Three
In this week we will cover Basic Data Types, ExpressionSet, biomaRt, and R S4.
9 个视频 （总计 79 分钟）, 1 个测验
9 个视频
Annotation Overview4分钟
ExpressionSet Overview4分钟
ExpressionSet9分钟
SummarizedExperiment7分钟
GEOquery6分钟
biomaRt13分钟
R S4 Classes16分钟
R S4 Methods10分钟
1 个练习
Quiz 320分钟
周
4Week Four
In this week, we will cover Getting data in Bioconductor, Rsamtools, oligo, limma, and minfi
7 个视频 （总计 81 分钟）, 1 个阅读材料, 1 个测验
7 个视频
Short Read4分钟
Rsamtools12分钟
oligo14分钟
limma16分钟
minfi11分钟
Count-based RNA-seq analysis15分钟
1 个阅读材料
Post Course Survey10分钟
1 个练习
Quiz 420分钟
4.0
33 个审阅热门审阅
创建者 MA•Mar 12th 2016
Excellent introduction to Bioconductor. Thanks to the team. However, absence of inputs from TA or Instructor was felt in the discussion.
创建者 AB•Apr 12th 2018
Amazing course, motivated me to use bio conductor for descriptive seq studies of DNA.
讲师
Kasper Daniel Hansen, PhD
Assistant Professor, Biostatistics and Genetic MedicineBloomberg School of Public Health
关于 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.
关于 Genomic Data Science 专项课程
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.
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