Bioconductor for Genomic Data Science

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

N Lecture Time Coursera Youtube Material Code Source
1 What is Bioconductor (7:18) Video Youtube PDF NA Google Slides
2 Installing Bioconductor (3:39) Video Youtube HTML NA R markdown (On GitHub)
3 The Bioconductor Website (9:56) Video Youtube HTML NA R markdown (On GitHub)
4 Useful Online Resources (5:08) Video Youtube HTML NA R markdown (On GitHub)
5 R Base Types (18:11) Video Youtube HTML R code R markdown (On GitHub)
6 GRanges – Overview (4:42) Video Youtube PDF NA Google Slides
7 IRanges – Basic Usage (12:12) Video Youtube HTML R code R markdown (On GitHub)
8 GenomicRanges – GRanges (8:44) Video Youtube HTML R code R markdown (On GitHub)
9 GenomicRanges – Basic GRanges Usage (8:14) Video Youtube HTML R code R markdown (On GitHub)
10 GenomicRanges – seqinfo (6:13) Video Youtube HTML R code R markdown (On GitHub)
11 AnnotationHub (8:23) Video Youtube HTML R code R markdown (On GitHub)
12 Usecase – AnnotationHub and GRanges, part 1 (12:56) Video Youtube HTML R code R markdown (On GitHub)
13 Usecase – AnnotationHub and GRanges, part 2 (13:46) Video Youtube HTML R code R markdown (On GitHub)
  Total (119:22)          

Week 2

N Lecture Time Coursea Youtube Material Code Source
14 Biostrings (7:04) Video Youtube HTML R code R markdown (On GitHub)
15 BSgenome (6:35) Video Youtube HTML R code R markdown (On GitHub)
16 Biostrings – Matching (6:18) Video Youtube HTML R code R markdown (On GitHub)
17 BSgenome – Views (9:21) Video Youtube HTML R code R markdown (On GitHub)
18 GenomicRanges – Rle (12:01) Video Youtube HTML R code R markdown (On GitHub)
19 GenomicRanges – Lists (8:02) Video Youtube HTML R code R markdown (On GitHub)
20 GenomicFeatures (18:30) Video Youtube HTML R code R markdown (On GitHub)
21 rtracklayer – Data Import (14:44) Video Youtube HTML R code R markdown (On GitHub)
  Total (82:35)          

Week 3

N Lecture Time Coursera Youtube Material Code Source
22 Basic Data Types (4:59) Video Youtube PDF NA Google Slides
23 Annotation Overview (4:33) Video Youtube PDF NA Google Slides
24 ExpressionSet Overview (4:19) Video Youtube PDF NA Google Slides
25 ExpressionSet (9:50) Video Youtube HTML R code R markdown (On GitHub)
26 SummarizedExperiment (7:44) Video Youtube HTML R code R markdown (On GitHub)
27 GEOquery (6:34) Video Youtube HTML R code R markdown (On GitHub)
28 biomaRt (13:48) Video Youtube HTML R code R markdown (On GitHub)
29 S4 Classes (16:56) Video Youtube HTML R code R markdown (On GitHub)
30 S4 Methods (10:15) Video Youtube HTML R code R markdown (On GitHub)
  Total (78:58)          

Week 4

N Lecture Time Coursera Youtube Material Code Source
31 Getting data into Bioconductor (6:32) Video Youtube HTML NA R markdown (On GitHub)
32 ShortRead (4:09) Video Youtube HTML R code R markdown (On GitHub)
33 Rsamtools (12:56) Video Youtube HTML R code R markdown (On GitHub)
0 oligo (14:19) Video Youtube HTML R code R markdown (On GitHub)
0 limma (16:38) Video Youtube HTML R code R markdown (On GitHub)
0 minfi (11:18) Video Youtube HTML R code R markdown (On GitHub)
0 Count Based RNAseq (15:34) Video Youtube HTML R code R markdown (On GitHub)
  Total (81:26)
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