====== Programming for Genomics ======

M2 ISG, 2015-2016

{{:members:pneuvial:teaching:isg:proggen.pdf|Introductory slides}}

===== Agenda =====

^ Date      ^ Title    ^ Materials          ^
| 11/19    | Data structures in R, by [[members:jchiquet:welcome|Julien Chiquet]]   | see [[http://julien.cremeriefamily.info/teachings_L3BI_ISV51.html|J. Chiquet's page]] |
| 11/27    | Naive approaches to segmentation |{{:members:pneuvial:teaching:isg:naive.rmd.zip|(zipped) .Rmd}}; {{:members:pneuvial:teaching:isg:naive.pdf|.pdf}} |
| 12/04    | Segmentation by dynamic programming 1 | {{:members:pneuvial:teaching:isg:dynamicprogramming.pdf|.pdf}}; {{:members:pneuvial:teaching:isg:20151204_dpseg.r.zip|R code}}|
| 12/11    | Advanced R programming| [[http://julien.cremeriefamily.info/doc/teachings/isv51/slides3-programmation.pdf|J. Chiquet's slides]]; [[http://dirk.eddelbuettel.com/papers/earl2015_boston_workshop.pdf|Slides by D. Eddelbuettel]] |
| 12/11    | Segmentation by dynamic programming 2 | {{:members:pneuvial:teaching:isg:dp_rcpp.pdf|Questions}}; {{:members:pneuvial:teaching:isg:dp_rcpp_solution.pdf|Solutions}};  {{:members:pneuvial:teaching:isg:dp_rccp_source.zip|Source files}}|
| 12/18    | Recursive binary segmentation + fused lasso| No notes available | 
| 12/18    | Reproducible research in genomics | {{:members:pneuvial:teaching:isg:201512_proggen_reproducibleresearch.pdf|Introduction (pdf)}}; [[http://bioinformatics.mdanderson.org/Supplements/ReproRsch-All/Modified/StarterSet/baggerly_nas_stanford_2012.pdf|Slides from K. Baggerly]]; [[http://www.cancerletter.com/articles/20150109_1|Recent news on the "Duke saga"]]| 
| 01/08    | **Exam** (1:00 PM-3:00 PM) | |

Some topics covered:

  * Computational/statistical tradeoffs when implementing statistical methods for genomic applications
  * Reproducible research 
  * Interfacing R code with C++
 


===== Links =====

  * Course [[http://julien.cremeriefamily.info/teachings_L3BI_ISV51.html|Introduction à la programmation]] by [[members:jchiquet:welcome|Julien Chiquet]] and references therein

R package repositories dedicated to genomics:
  * [[http://bioconductor.org|Bioconductor]]
  * [[http://aroma-project.org|The Aroma Project]]