À propos de ce cours : 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.
Créé par : Université Johns-Hopkins
Enseigné par : Kasper Daniel Hansen, PhD, Assistant Professor, Biostatistics and Genetic Medicine
Bloomberg School of Public Health
| Informations de base | Cours 6 de 8 dans Genomic Data Science Specialization |
| Langue | English |
| Comment réussir | Réussissez tous les devoirs notés pour terminer le cours. |
| Notes des utilisateurs |
Programme de cours
SEMAINE 1
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 vidéos, 3 lectures
- Reading: Welcome
- Reading: Syllabus
- Reading: Pre Course Survey
- Vidéo: Installing R on A Mac
- Vidéo: Installing R Studio on a Mac
- Vidéo: What is Bioconductor
- Vidéo: Installing Bioconductor
- Vidéo: The Bioconductor Website
- Vidéo: Useful Online Resources
- Vidéo: R Base Types
- Vidéo: GRanges - Overview
- Vidéo: IRanges - Basic Usage
- Vidéo: GenomicRanges - GRanges
- Vidéo: GenomicRanges - Basic GRanges Usage
- Vidéo: GenomicRanges - seqinfo
- Vidéo: AnnotationHub
- Vidéo: Usecase: AnnotationHub and GRanges, part 1
- Vidéo: Usecase: AnnotationHub and GRanges, part 2
Noté: Quiz 1
SEMAINE 2
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 vidéos
- Vidéo: BSgenome
- Vidéo: Biostrings - Matching
- Vidéo: BSgenome - Views
- Vidéo: GenomicRanges - Rle
- Vidéo: GenomicRanges - Lists
- Vidéo: GenomicFeatures
- Vidéo: rtracklayer - Data Import
Noté: Quiz 2
SEMAINE 3
Week Three
In this week we will cover Basic Data Types, ExpressionSet, biomaRt, and R S4.
9 vidéos
- Vidéo: Annotation Overview
- Vidéo: ExpressionSet Overview
- Vidéo: ExpressionSet
- Vidéo: SummarizedExperiment
- Vidéo: GEOquery
- Vidéo: biomaRt
- Vidéo: R S4 Classes
- Vidéo: R S4 Methods
Noté: Quiz 3
SEMAINE 4
Week Four
In this week, we will cover Getting data in Bioconductor, Rsamtools, oligo, limma, and minfi
7 vidéos, 1 lecture
- Vidéo: Short Read
- Vidéo: Rsamtools
- Vidéo: oligo
- Vidéo: limma
- Vidéo: minfi
- Vidéo: Count-based RNA-seq analysis
- Reading: Post Course Survey
Noté: Quiz 4
FAQ
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Coursework
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Créateurs
Université Johns-Hopkins
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.
Tarification
| Acheter le cours | |
|---|---|
| Accéder au contenu du cours | Disponible |
| Accéder au contenu noté | Disponible |
| Recevoir une Note Finale | Disponible |
| Obtenir un Certificat de Cours partageable | Disponible |
Notation et examens
It's very helpful in learning genomic data science. I think it's a little difficult in the beginning. The instructor have some accent, which made me even harder to get into it.
Good course, although some previous experience with R is required and that was not clearly stated beforehand. Moreover it would be better to have a more introductory course to R.
A great introduction to Bioconductor! The course is very hands-on, so be ready to use R extensively.
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The lessons are fairly easy to follow - although the transcript needs re-writing so that the correct words are identified to the speech. I spent a lot of time trying to decipher one or two key words.
The quizzes seemed to test on concepts not yet taught.. perhaps familiar to other Bioinformaticians.. so they were quite tough and required a lot of time to finish.