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Add simulations lecture #25

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Aug 24, 2023
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Add simulations lecture #25

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3 changes: 2 additions & 1 deletion .pre-commit-config.yaml
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Expand Up @@ -79,7 +79,8 @@ repos:
docs/slides/datageneration/index\.qmd|
docs/slides/foundations/index\.qmd|
docs/exercises/data_filtering/index\.qmd|
docs/slides/population_structure/index\.qmd
docs/slides/population_structure/index\.qmd|
docs/slides/simulation/index\.qmd
)$
minimum_pre_commit_version: "2.13.0"
- id: parsable-R
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1 change: 1 addition & 0 deletions docs/_quarto.yml
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Expand Up @@ -10,6 +10,7 @@ project:
render:
- "*.qmd"
- "!lectures/*.qmd"
- "*.ipynb"

website:
title: "Population genomics in practice"
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133 changes: 93 additions & 40 deletions docs/assets/bibliography.bib
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5 changes: 4 additions & 1 deletion docs/exercises/index.qmd
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Expand Up @@ -5,7 +5,10 @@ description: "List of all exercises"
listing:
type: grid
grid-columns: 4
fields: [image, title, author]
fields: [image, title, subtitle, author]
sort: false
contents:
- test/test.ipynb
date: ""
toc: false
sidebar: false
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100 changes: 50 additions & 50 deletions docs/schedule.qmd
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Expand Up @@ -24,56 +24,56 @@ format:

::: {.contents-table .column-body-outset}

| Topic | Time | Author | Links |
|------------------------------------------|-------------|------------|-----------------------------------------|
| [**6-Nov-2023 (Mon)**]{.highlight} | | | |
| Coffee and welcome | 08:30-09:00 | | |
| Introduction to PGIP | 09:00-09:30 | JH, NO, PU | |
| Population genomics in practice | 09:30-10:00 | PU | [Slides](slides/pgip/index.html) |
| Coffee break | 10:00-10:30 | | |
| Population genetics foundations | 10:30-12:00 | PU | [Slides](slides/foundations/index.html) |
| Lunch | 12:00-13:00 | | |
| Introduction to simulation | 13:00-15:00 | PU | Slides, Exercise |
| Coffee break | 15:00-15:30 | | |
| Introduction to simulation | 15:30-17:00 | PU | Slides, Exercise |
| [**7-Nov-2023 (Tue)**]{.highlight} | | | |
| Recap day 1 | 09:00-09:30 | PU | |
| Variant calling and filtering | 09:30-10:00 | PU | Slides, Exercise |
| Coffee break | 10:00-10:30 | | |
| Variant calling and filtering, continued | 10:30-12:00 | PU | Slides, Exercise |
| Lunch | 12:00-13:00 | | |
| Genetic diversity | 13:00-15:00 | PU | Slides, Exercise |
| Coffee break | 15:00-15:30 | | |
| TBA | 15:30-17:00 | | |
| [**8-Nov-2023 (Wed)**]{.highlight} | | | |
| Recap day 2 | 09:00-09:30 | PU | |
| PCA | 09:30-10:00 | | |
| Coffee break | 10:00-10:30 | | |
| Fst | 10:30-12:00 | | |
| Lunch | 12:00-13:00 | | |
| Admixture | 13:00-15:00 | | |
| Coffee break | 15:00-15:30 | | |
| f-statistics | 15:30-17:00 | | |
| | | | |
| [**9-Nov-2023 (Thu)**]{.highlight} | | | |
| Recap day 3 | 09:00-09:30 | | |
| Demography | 09:30-10:00 | | |
| Coffee break | 10:00-10:30 | | |
| Demography and psmc | 10:30-12:00 | | |
| Lunch | 12:00-13:00 | | |
| Selection | 13:00-15:00 | | |
| Coffee break | 15:00-15:30 | | |
| Selection | 15:30-17:00 | | |
| | | | |
| [**10-Nov-2023 (Fri)**]{.highlight} | | | |
| Recap | 09:00-10:00 | JH, NO, PU | |
| Coffee break | 10:00-10:30 | | |
| Guest lecture | 10:30-11:30 | | |
| Recap continued | 11:30-12:00 | JH, NO, PU | |
| Lunch | 12:00-13:00 | | |
| Guest lecture | 13:00-14:00 | | |
| Recap continued | 14:00-15:00 | JH, NO, PU | |
| Project discussion | 15:00-17:00 | | |
| Topic | Time | Author | Links |
|------------------------------------------|-------------|------------|----------------------------------------------------------------------------------------------------------|
| [**6-Nov-2023 (Mon)**]{.highlight} | | | |
| Coffee and welcome | 08:30-09:00 | | |
| Introduction to PGIP | 09:00-09:30 | JH, NO, PU | |
| Population genomics in practice | 09:30-10:00 | PU | [Slides](slides/pgip/index.html) |
| Coffee break | 10:00-10:30 | | |
| Population genetics foundations | 10:30-12:00 | PU | [Slides](slides/foundations/index.html) |
| Lunch | 12:00-13:00 | | |
| Introduction to simulation | 13:00-15:00 | PU | [Slides](slides/simulation/index.html), [Exercise](https://percyfal.github.io/pgip-jlite/lab/index.html) |
| Coffee break | 15:00-15:30 | | |
| Introduction to simulation | 15:30-17:00 | PU | [Slides](slides/simulation/index.html), [Exercise](https://percyfal.github.io/pgip-jlite/lab/index.html) |
| [**7-Nov-2023 (Tue)**]{.highlight} | | | |
| Recap day 1 | 09:00-09:30 | PU | |
| Variant calling and filtering | 09:30-10:00 | PU | Slides, Exercise |
| Coffee break | 10:00-10:30 | | |
| Variant calling and filtering, continued | 10:30-12:00 | PU | Slides, Exercise |
| Lunch | 12:00-13:00 | | |
| Genetic diversity | 13:00-15:00 | PU | Slides, Exercise |
| Coffee break | 15:00-15:30 | | |
| TBA | 15:30-17:00 | | |
| [**8-Nov-2023 (Wed)**]{.highlight} | | | |
| Recap day 2 | 09:00-09:30 | PU | |
| PCA | 09:30-10:00 | | |
| Coffee break | 10:00-10:30 | | |
| Fst | 10:30-12:00 | | |
| Lunch | 12:00-13:00 | | |
| Admixture | 13:00-15:00 | | |
| Coffee break | 15:00-15:30 | | |
| f-statistics | 15:30-17:00 | | |
| | | | |
| [**9-Nov-2023 (Thu)**]{.highlight} | | | |
| Recap day 3 | 09:00-09:30 | | |
| Demography | 09:30-10:00 | | |
| Coffee break | 10:00-10:30 | | |
| Demography and psmc | 10:30-12:00 | | |
| Lunch | 12:00-13:00 | | |
| Selection | 13:00-15:00 | | |
| Coffee break | 15:00-15:30 | | |
| Selection | 15:30-17:00 | | |
| | | | |
| [**10-Nov-2023 (Fri)**]{.highlight} | | | |
| Recap | 09:00-10:00 | JH, NO, PU | |
| Coffee break | 10:00-10:30 | | |
| Guest lecture | 10:30-11:30 | | |
| Recap continued | 11:30-12:00 | JH, NO, PU | |
| Lunch | 12:00-13:00 | | |
| Guest lecture | 13:00-14:00 | | |
| Recap continued | 14:00-15:00 | JH, NO, PU | |
| Project discussion | 15:00-17:00 | | |

:::

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