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index.Rmd
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---
title: "Bioconductor for Genomic Data Science"
---
**Instructor:** [Kasper Daniel Hansen](http://www.hansenlab.org/)
**Class Website:**
* [Bioconductor for Genomic Data Science](https://www.coursera.org/course/genbioconductor)
* [Genomic Data Science Specialization](https://www.coursera.org/specialization/genomics/41)
### **Resources**
Videos and material were prepared using the following software
- R version 3.2.1 (available from [CRAN](https://cran.r-project.org/)).
- RStudio version 0.99.467 (available from [RStudio](https://www.rstudio.com)).
- Bioconductor version 3.1.
Installation help
- Installing R for Windows ([Youtube](https://youtu.be/Ohnk9hcxf9M))
- Installing R for Mac ([Youtube](https://youtu.be/uxuuWXU-7UQ))
- Installing RStudio Mac ([Youtube](https://youtu.be/bM7Sfz-LADM))
Other sources of help
- [RStudio](https://www.rstudio.com/), [R project](http://www.r-project.org/), and [Bioconductor](http://bioconductor.org/)
- [RStudio's cheatsheets](https://www.rstudio.com/resources/cheatsheets/)
- [PH525x Statistics for Genomics Book](http://genomicsclass.github.io/book/)
### Course Materials
All materials are available on the Coursera website as well as on the course [GitHub page](http://kasperdanielhansen.github.io/genbioconductor/). 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](http://www.coursera.org/course/genbioconductor) website as well as on [Youtube](http://www.youtube.com). Links are provided to both locations.
#### Week 1
| N | Lecture | Time | Coursera | Youtube | Material | Code | Source |
|---|---|---|---|---|--|--|--|
| 1 | What is Bioconductor | (7:18) | [Video](COURSERA_URL/5) | [Youtube](https://youtu.be/ScOQ9XHHAH0) | [PDF](pdf/BiocIntro_What_is_Bioconductor.pdf) | NA | [Google Slides](https://docs.google.com/presentation/d/1rPKLk9tTfoLkRl-PyaboJ4wHTsLhmm2ukBRxOmJg4Kk/edit?usp=sharing) |
| 2 | Installing Bioconductor | (3:39) | [Video](COURSERA_URL/7) | [Youtube](https://youtu.be/dyPbaLpevGw) | [HTML](html/Install_Bioconductor.html) | NA | [R markdown](Rmd/Install_Bioconductor.Rmd) ([On GitHub](GITHUB_URL/Install_Bioconductor.Rmd)) |
| 3 | The Bioconductor Website | (9:56) | [Video](COURSERA_URL/9) | [Youtube](https://youtu.be/TIj2ckwJmqM) | [HTML](html/Online_Resources.html) | NA | [R markdown](Rmd/Online_Resources.Rmd) ([On GitHub](GITHUB_URL/Online_Resources.Rmd)) |
| 4 | Useful Online Resources | (5:08) | [Video](COURSERA_URL/11) | [Youtube](https://youtu.be/290_-Ca5iAk) | [HTML](html/Online_Resources.html) | NA | [R markdown](Rmd/Online_Resources.Rmd) ([On GitHub](GITHUB_URL/Online_Resources.Rmd)) |
| 5 | R Base Types | (18:11) | [Video](COURSERA_URL/13) | [Youtube](https://youtu.be/x75azcLzQzs) | [HTML](html/R_Base_Types.html) | [R code](R/R_Base_Types.R) | [R markdown](Rmd/R_Base_Types.Rmd) ([On GitHub](GITHUB_URL/R_Base_Types.Rmd)) |
| 6 | GRanges - Overview | (4:42) | [Video](COURSERA_URL/15) | [Youtube](https://youtu.be/ET7NBhXZEoI) | [PDF](pdf/BiocIntro_GRanges_Overview.pdf) | NA | [Google Slides](https://docs.google.com/presentation/d/1ETjUipnle-Ps7k8gFGvJIXJ85D_Vjs9qNxNk2KeeaAI/edit?usp=sharing) |
| 7 | IRanges - Basic Usage | (12:12) | [Video](COURSERA_URL/17) | [Youtube](https://youtu.be/YB2WRH3sFHs) | [HTML](html/IRanges_Basic.html) | [R code](R/IRanges_Basic.R) | [R markdown](Rmd/IRanges_Basic.Rmd) ([On GitHub](GITHUB_URL/IRanges_Basic.Rmd)) |
| 8 | GenomicRanges - GRanges | (8:44) | [Video](COURSERA_URL/19) | [Youtube](https://youtu.be/et3zeBXnpdc) | [HTML](html/GenomicRanges_GRanges.html) | [R code](R/GenomicRanges_GRanges.R) | [R markdown](Rmd/GenomicRanges_GRanges.Rmd) ([On GitHub](GITHUB_URL/GenomicRanges_GRanges.Rmd)) |
| 9 | GenomicRanges - Basic GRanges Usage | (8:14) | [Video](COURSERA_URL/21) | [Youtube](https://youtu.be/dxoIvuRLGuk) | [HTML](html/GenomicRanges_GRanges_Usage.html) | [R code](R/GenomicRanges_GRanges_Usage.R) | [R markdown](Rmd/GenomicRanges_GRanges_Usage.Rmd) ([On GitHub](GITHUB_URL/GenomicRanges_GRanges_Usage.Rmd)) |
| 10 | GenomicRanges - seqinfo | (6:13) | [Video](COURSERA_URL/23) | [Youtube](https://youtu.be/nEJIvoUmuBM) | [HTML](html/GenomicRanges_seqinfo.html) | [R code](R/GenomicRanges_seqinfo.R) | [R markdown](Rmd/GenomicRanges_seqinfo.Rmd) ([On GitHub](GITHUB_URL/GenomicRanges_seqinfo.Rmd)) |
| 11 | AnnotationHub | (8:23) | [Video](COURSERA_URL/25) | [Youtube](https://youtu.be/bw55cuD6bqA) | [HTML](html/AnnotationHub.html) | [R code](R/AnnotationHub.R) | [R markdown](Rmd/AnnotationHub.Rmd) ([On GitHub](GITHUB_URL/AnnotationHub.Rmd)) |
| 12 | Usecase - AnnotationHub and GRanges, part 1 | (12:56) | [Video](COURSERA_URL/27) | [Youtube](https://youtu.be/5XVfLe8GtdI) | [HTML](html/Usecase_AnnotationHub_GRanges.html) | [R code](R/Usecase_AnnotationHub_GRanges.R) | [R markdown](Rmd/Usecase_AnnotationHub_GRanges.Rmd) ([On GitHub](GITHUB_URL/Usecase_AnnotationHub_GRanges.Rmd)) |
| 13 | Usecase - AnnotationHub and GRanges, part 2 | (13:46) | [Video](COURSERA_URL/29) | [Youtube](https://youtu.be/08r_l0x4L1k) | [HTML](html/Usecase_AnnotationHub_GRanges.html) | [R code](R/Usecase_AnnotationHub_GRanges.R) | [R markdown](Rmd/Usecase_AnnotationHub_GRanges.Rmd) ([On GitHub](GITHUB_URL/Usecase_AnnotationHub_GRanges.Rmd)) |
| | Total | (119:22) | | | | | |
#### Week 2
| N | Lecture | Time | Coursea | Youtube | Material | Code | Source |
|---|---|---|---|---|--|--|--|
| 14 | Biostrings | (7:04) | [Video](COURSERA_URL/43) | [Youtube](https://youtu.be/lTXsZ1glvUY) | [HTML](html/Biostrings.html) | [R code](R/Biostrings.R) | [R markdown](Rmd/Biostrings.Rmd) ([On GitHub](GITHUB_URL/Biostrings.Rmd)) |
| 15 | BSgenome | (6:35) | [Video](COURSERA_URL/45) | [Youtube](https://youtu.be/cNJ2wbObRl8) | [HTML](html/BSgenome.html) | [R code](R/BSgenome.R) | [R markdown](Rmd/BSgenome.Rmd) ([On GitHub](GITHUB_URL/BSgenome.Rmd)) |
| 16 | Biostrings - Matching | (6:18) | [Video](COURSERA_URL/47) | [Youtube](https://youtu.be/wFfaF4M8sqM) | [HTML](html/Biostrings_Matching.html) | [R code](R/Biostrings_Matching.R) | [R markdown](Rmd/Biostrings_Matching.Rmd) ([On GitHub](GITHUB_URL/Biostrings_Matching.Rmd)) |
| 17 | BSgenome - Views | (9:21) | [Video](COURSERA_URL/49) | [Youtube](https://youtu.be/fPBxqAPXQCE) | [HTML](html/BSgenome_Views.html) | [R code](R/BSgenome_Views.R) | [R markdown](Rmd/BSgenome_Views.Rmd) ([On GitHub](GITHUB_URL/BSgenome_Views.Rmd)) |
| 18 | GenomicRanges - Rle | (12:01) | [Video](COURSERA_URL/51) | [Youtube](https://youtu.be/w7ZPnO-jB9o) | [HTML](html/GenomicRanges_Rle.html) | [R code](R/GenomicRanges_Rle.R) | [R markdown](Rmd/GenomicRanges_Rle.Rmd) ([On GitHub](GITHUB_URL/GenomicRanges_Rle.Rmd)) |
| 19 | GenomicRanges - Lists | (6:02) | [Video](COURSERA_URL/53) | [Youtube](https://youtu.be/Ba3_nX2L1gI) | [HTML](html/GenomicRanges_Lists.html) | [R code](R/GenomicRanges_Lists.R) | [R markdown](Rmd/GenomicRanges_Lists.Rmd) ([On GitHub](GITHUB_URL/GenomicRanges_Lists.Rmd)) |
| 20 | GenomicFeatures | (18:30) | [Video](COURSERA_URL/55) | [Youtube](https://youtu.be/9sAhB4Bs43k) | [HTML](html/GenomicFeatures.html) | [R code](R/GenomicFeatures.R) | [R markdown](Rmd/GenomicFeatures.Rmd) ([On GitHub](GITHUB_URL/GenomicFeatures.Rmd)) |
| 21 | rtracklayer - Data Import | (14:44) | [Video](COURSERA_URL/57) | [Youtube](https://youtu.be/BGlXm0kCwf4) | [HTML](html/rtracklayer_Import.html) | [R code](R/rtracklayer_Import.R) | [R markdown](Rmd/rtracklayer_Import.Rmd) ([On GitHub](GITHUB_URL/rtracklayer_Import.Rmd)) |
| | Total | (80:35) | | | | | |
#### Week 3
| N | Lecture | Time | Coursera | Youtube | Material | Code | Source |
|---|---|---|---|---|--|--|--|
| 22 | Basic Data Types | (4:59) | [Video](COURSERA_URL/31) | [Youtube](https://youtu.be/bkyPZxpqALQ) | [PDF](pdf/BiocIntro_Basic_Data_Types.pdf) | NA | [Google Slides](https://docs.google.com/presentation/d/1GidGTxreaffyutdpy4vKcmKdWc-z1KYsWbxihTorI_8/edit?usp=sharing) |
| 23 | Annotation Overview | (4:33) | [Video](COURSERA_URL/35) | [Youtube](https://youtu.be/_0I3l_DfaEU) | [PDF](pdf/BiocIntro_Annotation_Overview.pdf) | NA | [Google Slides](https://docs.google.com/presentation/d/14-uvs23suNXr8-xZRDcreo_Ws01VKCLCUy-q99Gf_hc/edit?usp=sharing) |
| 24 | ExpressionSet Overview | (4:19) | [Video](COURSERA_URL/33) | [Youtube](https://youtu.be/5EAOwLDD6Wo) | [PDF](pdf/BiocIntro_ExpressionSet_Overview.pdf) | NA |[Google Slides](https://docs.google.com/presentation/d/1ouDEq37R5ReiuLgfSm7c3lexceIovy5IUac9jfYX1L8/edit?usp=sharing) |
| 25 | ExpressionSet | (9:50) | [Video](COURSERA_URL/37) | [Youtube](https://youtu.be/wVFxRsz2zGQ) | [HTML](html/ExpressionSet.html) | [R code](R/ExpressionSet.R) | [R markdown](Rmd/ExpressionSet.Rmd) ([On GitHub](GITHUB_URL/ExpressionSet.Rmd)) |
| 26 | SummarizedExperiment | (7:44) | [Video](COURSERA_URL/39) | [Youtube](https://youtu.be/D8IVRmbMjyc) | [HTML](html/SummarizedExperiment.html) | [R code](R/SummarizedExperiment.R) | [R markdown](Rmd/SummarizedExperiment.Rmd) ([On GitHub](GITHUB_URL/SummarizedExperiment.Rmd)) |
| 27 | GEOquery | (6:34) | [Video](COURSERA_URL/41) | [Youtube](https://youtu.be/hO4ORyp9FDo) | [HTML](html/GEOquery.html) | [R code](R/GEOquery.R) | [R markdown](Rmd/GEOquery.Rmd) ([On GitHub](GITHUB_URL/GEOquery.Rmd)) |
| 28 | biomaRt | (13:48) | [Video](COURSERA_URL/61) | [Youtube](https://youtu.be/-EXanoy2CGk) | [HTML](html/biomaRt.html) | [R code](R/biomaRt.R) | [R markdown](Rmd/biomaRt.Rmd) ([On GitHub](GITHUB_URL/biomaRt.Rmd)) |
| 29 | S4 Classes | (16:56) | [Video](COURSERA_URL/63) | [Youtube](https://youtu.be/CeP-A__FroY) | [HTML](html/R_S4.html) | [R code](R/R_S4.R) | [R markdown](Rmd/R_S4.Rmd) ([On GitHub](GITHUB_URL/R_S4.Rmd)) |
| 30 | S4 Methods | (10:15) | [Video](COURSERA_URL/65) | [Youtube](https://youtu.be/wm-VCagXwj4) | [HTML](html/R_S4.html) | [R code](R/R_S4.R) | [R markdown](Rmd/R_S4.Rmd) ([On GitHub](GITHUB_URL/R_S4.Rmd)) |
| | Total | (78:58) | | | | | |
#### Week 4
| N | Lecture | Time | Coursera | Youtube | Material | Code | Source |
|---|---|---|---|---|--|--|--|
| 31 | Getting data into Bioconductor | (6:32) | [Video](COURSERA_URL/73) | [Youtube](https://youtu.be/mXg_YqSVpwM) | [HTML](html/Getting_Data_into_Bioconductor.html) | NA | [R markdown](Rmd/Getting_Data_into_Bioconductor.Rmd) ([On GitHub](GITHUB_URL/Getting_Data_into_Bioconductor.Rmd))
| 32 | ShortRead | (4:09) | [Video](COURSERA_URL/75) | [Youtube](https://youtu.be/dEDlER0ZNfA) | [HTML](html/ShortRead.html) | [R code](R/ShortRead.R) | [R markdown](Rmd/ShortRead.Rmd) ([On GitHub](GITHUB_URL/ShortRead.Rmd))
| 33 | Rsamtools | (12:56) | [Video](COURSERA_URL/77) | [Youtube](https://youtu.be/3T4mDPQ5hU8) | [HTML](html/Rsamtools.html) | [R code](R/Rsamtools.R) | [R markdown](Rmd/Rsamtools.Rmd) ([On GitHub](GITHUB_URL/Rsamtools.Rmd))
| 34 | oligo | (14:19) | [Video](COURSERA_URL/81) | [Youtube](https://youtu.be/_pAtq0OC8Ro) | [HTML](html/oligo.html) | [R code](R/oligo.R) | [R markdown](Rmd/oligo.Rmd) ([On GitHub](GITHUB_URL/oligo.Rmd))
| 35 | limma | (16:38) | [Video](COURSERA_URL/79) | [Youtube](https://youtu.be/ZRet1oeGiUU) | [HTML](html/limma.html) | [R code](R/limma.R) | [R markdown](Rmd/limma.Rmd) ([On GitHub](GITHUB_URL/limma.Rmd))
| 36 | minfi | (11:18) | [Video](COURSERA_URL/83) | [Youtube](https://youtu.be/0llfypt9FAM) | [HTML](html/minfi.html) | [R code](R/minfi.R) | [R markdown](Rmd/minfi.Rmd) ([On GitHub](GITHUB_URL/minfi.Rmd))
| 37 | Count Based RNAseq | (15:34) | [Video](COURSERA_URL/85) | [Youtube](https://youtu.be/zAXHn_Y_NhI) | [HTML](html/Count_Based_RNAseq.html) | [R code](R/Count_Based_RNAseq.R) | [R markdown](Rmd/Count_Based_RNAseq.Rmd) ([On GitHub](GITHUB_URL/Count_Based_RNAseq.Rmd))
| | Total | (81:26) | | | | | |
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