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.
提供方
教學大綱 - 您將從這門課程中學到什麼
週
1完成時間為 3 小時
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 個視頻 （總計 126 分鐘）, 3 個閱讀材料, 1 個測驗
16 個視頻
Installing R on A Mac 2分鐘
Installing R Studio on a Mac 1分鐘
What is Bioconductor7分鐘
Installing Bioconductor3分鐘
The Bioconductor Website9分鐘
Useful Online Resources5分鐘
R Base Types18分鐘
GRanges - Overview4分鐘
IRanges - Basic Usage12分鐘
GenomicRanges - GRanges8分鐘
GenomicRanges - Basic GRanges Usage8分鐘
GenomicRanges - seqinfo6分鐘
AnnotationHub8分鐘
Usecase: AnnotationHub and GRanges, part 112分鐘
Usecase: AnnotationHub and GRanges, part 213分鐘
3 個閱讀材料
Welcome10分鐘
Syllabus10分鐘
Pre Course Survey10分鐘
1 個練習
Quiz 120分鐘
週
2完成時間為 2 小時
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 個視頻 （總計 81 分鐘）, 1 個測驗
8 個視頻
Biostrings7分鐘
BSgenome6分鐘
Biostrings - Matching6分鐘
BSgenome - Views9分鐘
GenomicRanges - Rle12分鐘
GenomicRanges - Lists6分鐘
GenomicFeatures18分鐘
rtracklayer - Data Import14分鐘
1 個練習
Quiz 220分鐘
週
3完成時間為 2 小時
Week Three
In this week we will cover Basic Data Types, ExpressionSet, biomaRt, and R S4.
9 個視頻 （總計 79 分鐘）, 1 個測驗
9 個視頻
Annotation Overview4分鐘
ExpressionSet Overview4分鐘
ExpressionSet9分鐘
SummarizedExperiment7分鐘
GEOquery6分鐘
biomaRt13分鐘
R S4 Classes16分鐘
R S4 Methods10分鐘
1 個練習
Quiz 320分鐘
週
4完成時間為 2 小時
Week Four
In this week, we will cover Getting data in Bioconductor, Rsamtools, oligo, limma, and minfi
7 個視頻 （總計 81 分鐘）, 1 個閱讀材料, 1 個測驗
7 個視頻
Short Read4分鐘
Rsamtools12分鐘
oligo14分鐘
limma16分鐘
minfi11分鐘
Count-based RNA-seq analysis15分鐘
1 個閱讀材料
Post Course Survey10分鐘
1 個練習
Quiz 420分鐘
4.0
38 個審閱來自使用Bioconductor分析基因组科学数据的熱門評論
Before you can run, you must learn to walk.\n\nKasper's well paced tutorials will give you confidence using the tools you need for genomic study.
Excellent introduction to Bioconductor. Thanks to the team. However, absence of inputs from TA or Instructor was felt in the discussion.
講師
Kasper Daniel Hansen, PhD
Assistant Professor, Biostatistics and Genetic MedicineBloomberg School of Public Health
關於 约翰霍普金斯大学
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.
關於 基因组数据科学 專項課程
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.
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