Difference between revisions of "UNIL BSc course: Bioinformatics for Genomics 2023"
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** [[User:Daniel|Daniel]] | ** [[User:Daniel|Daniel]] | ||
** [[User:Sofia|Sofia]] | ** [[User:Sofia|Sofia]] | ||
| + | ** [[User:Ilaria|Ilaria]] | ||
* Schedule | * Schedule | ||
** 29 March 2023: "Measuring and visualising genome-wide gene expression" | ** 29 March 2023: "Measuring and visualising genome-wide gene expression" | ||
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven) | *** 8:30-10:00 [https://docs.google.com/presentation/d/1_yeaGCdQXquVOxiWjYd1hsWewQF5G0uWHvhoOdUMvIQ/edit?usp=sharing Lecture] (Sven) | ||
| − | *** 10:30-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Sven) | + | *** 10:30-12:00 [https://drive.google.com/file/d/1O4BCJ-zn76kLhpVa8Bs-GVh6OVpn2m_x/view?usp=sharing Tutorial] (Lead: Olga, Support: Michael, Ilaria, Sven) |
** 5 April 2023: "Advanced analysis of genome-wide gene expression" | ** 5 April 2023: "Advanced analysis of genome-wide gene expression" | ||
*** 8:30-10:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven) | *** 8:30-10:00 [https://docs.google.com/presentation/d/1UoT62e1OwNNOt-NN4O3ZDALM_9GW3l_o0_vMLAZoSns/edit?usp=sharing Lecture] (Sven) | ||
| − | *** 10:30-12:00 Tutorial (Lead: Michael, Support: Olga, Sven) | + | *** 10:30-12:00 [https://drive.google.com/file/d/1SyXmU1ePrJTkBQl1uNRqwg6NFlmtQNEQ/view?usp=sharing Tutorial] (Lead: Michael, Support: Olga, Ilaria, Sven) |
** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles" | ** 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles" | ||
*** 8:30-10:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven) | *** 8:30-10:00 [https://docs.google.com/presentation/d/1vb3RTd8yaSJOPHDX92G-hmb40DtABRzYgf_HqzK2HP4/edit?usp=sharing Lecture] (Sven) | ||
| − | *** 10:30-12:00 Tutorial (Lead: Anneke, Support: Daniel, Sven) | + | *** 10:30-12:00 [https://colab.research.google.com/drive/1GsazMsMxtEHxWYYMkGXqyb47RJTDsPeR?usp=sharing Tutorial] (Lead: Anneke, Support: Daniel, Ilaria, Sven) |
** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts" | ** 26 April 2023: "Measuring and visualising genome-wide chromatin contacts" | ||
*** 8:30-10:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven) | *** 8:30-10:00 [https://docs.google.com/presentation/d/1_U455VPcY7atVF65ePM7IMYwXVzndiVUAy1lszXpCj4/edit?usp=sharing Lecture] (Sven) | ||
| − | *** 10:30-12:00 Tutorial (Lead: Daniel, Support: Sofia, Sven) | + | *** 10:30-12:00 [https://colab.research.google.com/drive/1FDlKl1iuNQYb4wc11Lgdj1s98SzfBDOb?usp=sharing Tutorial] (Lead: Daniel, Support: Sofia, Ilaria, Sven) |
** 27 April 2023: "Defining and visualising gene networks" | ** 27 April 2023: "Defining and visualising gene networks" | ||
| − | *** 14:00-15:30 Lecture (Sven) | + | *** 14:00-15:30 [https://docs.google.com/presentation/d/1LpSUx5nQaQCWQXqzWdNfarFA1ha6JMyeC-q5Nf_RfPQ/edit?usp=sharing Lecture] (Sven) |
| − | *** 16:00-17:30 Tutorial (Lead: Sofia, Support: Anneke, Sven) | + | *** 16:00-17:30 [https://colab.research.google.com/drive/1V6iKh0zLhe7Ofxx5aN40MYzNsJ4O3pJk?usp=sharing Tutorial] (Lead: Sofia, Support: Anneke, Ilaria, Sven) |
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course. | We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course. | ||
Latest revision as of 21:03, 26 April 2023
This course is for third year B.Sc. students and part of the "Genetics and Genome evolution" (GGE) module.
- Course aims:
- Get to know some key bioinformatics methods necessary for genomic analysis
- Apply these methods, focusing on data-visualisation (typically trying to reproduce selected figures that where discussed in other GGE courses)
- Develop an understanding of potential pitfalls and the impact of bioinformatics choices in genomic results
- Prerequisites:
- Notions of genomics (gene, genome, transcriptome)
- Basic statistics (what is a test, a p-value)
- Basic literacy in R and/or Python.
- Teacher: Sven Bergmann
- Schedule
- 29 March 2023: "Measuring and visualising genome-wide gene expression"
- 5 April 2023: "Advanced analysis of genome-wide gene expression"
- 19 April 2023: "Measuring and visualising genome-wide epigenetic profiles"
- 26 April 2023: "Measuring and visualising genome-wide chromatin contacts"
- 27 April 2023: "Defining and visualising gene networks"
We will hand out one exercise for each tutorial. Students will start working on these exercises in the tutorial session and will need to submit their answers within one week. The submissions will be graded and count for the grade of this course.
