BY.Tan

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Bioconductor for Genomic Data Science

波比 / 2016-06-06


Course Materials

All materials are available on the Coursera website as well as on the course GitHub page. The materials on the GitHub website will be updated continuously as needed, whereas the materials hosted on Coursera will not change after the course has started. The course consists of a number of video lecture. Most of the video lectures are supported by a script in R markdown which we render in HTML and we provide the stand-alone R code. We recommend reading these lectures following the HTML links. Changes and improvements to these scripts are welcome at the class GitHub repository. There is a few number of video lectures supported by slides made in Google Slides. We link to the original slides and provide them in HTML. Videos are available both on the Coursera website as well as on Youtube. Links are provided to both locations.

Week 1

  1. What is Bioconductor (7:18)

Video

Youtube

PDF

Google Slides

  1. Installing Bioconductor (3:39)

Video

Youtube

HTML

R markdown (On GitHub)

  1. The Bioconductor Website (9:56)

Video

Youtube

HTML

R markdown (On GitHub)

  1. Useful Online Resources (5:08)

Video

Youtube

HTML

R markdown (On GitHub)

  1. R Base Types (18:11)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. GRanges - Overview (4:42)

Video

Youtube

PDF

Google Slides

  1. IRanges - Basic Usage (12:12)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. GenomicRanges - GRanges (8:44)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. GenomicRanges - Basic GRanges Usage (8:14)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. GenomicRanges - seqinfo (6:13)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. AnnotationHub (8:23)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. Usecase - AnnotationHub and GRanges, part 1 (12:56)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. Usecase - AnnotationHub and GRanges, part 2 (13:46)

Video

Youtube

HTML

R code

R markdown (On GitHub)

Week 2

  1. Biostrings (7:04)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. BSgenome (6:35)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. Biostrings - Matching (6:18)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. BSgenome - Views (9:21)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. GenomicRanges - Rle (12:01)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. GenomicRanges - Lists (8:02)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. GenomicFeatures (18:30)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. rtracklayer - Data Import (14:44)

Video

Youtube

HTML

R code

R markdown (On GitHub)

Week 3

  1. Basic Data Types (4:59)

Video

Youtube

PDF

Google Slides

  1. Annotation Overview (4:33)

Video

Youtube

PDF

Google Slides

  1. ExpressionSet Overview (4:19)

Video

Youtube

PDF

Google Slides

  1. ExpressionSet (9:50)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. SummarizedExperiment (7:44)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. GEOquery (6:34)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. biomaRt (13:48)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. S4 Classes (16:56)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. S4 Methods (10:15)

Video

Youtube

HTML

R code

R markdown (On GitHub)

Week 4

  1. Getting data into Bioconductor (6:32)

Video

Youtube

HTML

R markdown (On GitHub)

  1. ShortRead (4:09)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. Rsamtools (12:56)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. oligo (14:19)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. limma (16:38)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. minfi (11:18)

Video

Youtube

HTML

R code

R markdown (On GitHub)

  1. Count Based RNAseq (15:34)

Video

Youtube

HTML

R code

R markdown (On GitHub)