Instructor: Kasper Daniel Hansen
Class Website:
Videos and material were prepared using the following software
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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.
| N | Lecture | Time | Coursera | Youtube | Material | Code | Source |
|---|---|---|---|---|---|---|---|
| 1 | What is Bioconductor | (7:18) | Video | Youtube | 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 | 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) |
| 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) |
| N | Lecture | Time | Coursera | Youtube | Material | Code | Source |
|---|---|---|---|---|---|---|---|
| 22 | Basic Data Types | (4:59) | Video | Youtube | NA | Google Slides | |
| 23 | Annotation Overview | (4:33) | Video | Youtube | NA | Google Slides | |
| 24 | ExpressionSet Overview | (4:19) | Video | Youtube | 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) |
| 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) |
This page was last updated on 2015-09-07 08:44:29 Eastern Time.