initial setup

README.md

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-# SISG_2024
+# SISG_2023
+
+Course materials for SISG Module 18: Computational Pipeline for WGS Data, July 26-28, 2023
+
+See the rendered website at
+[https://uw-gac.github.io/SISG_2023](https://uw-gac.github.io/SISG_2023)

_config.yml

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+#theme: jekyll-theme-minimal
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+title: SISG Module 18 | Computational Pipeline for WGS Data
+
+description: July 26-28, 2023

index.md

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+This site contains course materials for SISG Module 18: Computational Pipeline for WGS Data, July 26-28, 2023. **Course evaluations and certificates of completion will be available via the [official SISG course web page](https://si.biostat.washington.edu/institutes/sisg/SM2318)** (requires login).
+
+- **Instructors:** Ken Rice, Laura Raffield, and Matthew Conomos
+- **[Join the Slack Discussion](https://uwbiostatisticssisg.slack.com/archives/C05EAUXKLUT)**
+
+## Course Format
+
+#### Lectures
+Course material will be presented through lectures. Slides for lectures are linked in the schedule below.
+
+#### Exercises
+Many of the lectures will be followed with hands-on exercises. Students are encouraged to work through the exercises together. Afterwards, the instructors will walk through the exercises and lead a discussion.
+
+To run the exercises, log into [NHLBI BioData Catalyst powered by Seven Bridges](https://platform.sb.biodatacatalyst.nhlbi.nih.gov) with your username and password -- we will use this platform for live demonstrations during the course.
+
+- You will retain access to the Seven Bridges platform, including your SISG Project with all of the course materials even after the course ends. The SISG23 Workshop billing group will remain available to you for a short period of time, after which you will need to set up another payment method to run analyses. You can [request pilot cloud credits](https://biodatacatalyst.nhlbi.nih.gov/resources/cloud-credits) ($500 worth) from BioData Catalyst. Additionally, there is guidance available for [writing BioData Catalyst cloud costs into your grant proposal budget](https://bdcatalyst.gitbook.io/biodata-catalyst-documentation/written-documentation/getting-started/writing-biodata-catalyst-into-a-grant-proposal). 
+
+All of the R code and data can also be downloaded from the [github repository](https://github.com/UW-GAC/SISG_2023) from which the site is built and run on your local machine. Download the complete workshop data and exercises: [https://github.com/UW-GAC/SISG_2023/archive/main.zip](https://github.com/UW-GAC/SISG_2023/archive/main.zip)
+
+
+## Schedule
+
+NOTE: All times are Pacific Daylight Time (GMT-07:00)
+
+**Wednesday, July 26th**
+
+| Time | Topic | Lecture | Exercises/Discussion |
+| --- | --- | --- | --- |
+| 1:30pm-1:40pm | Introduction | Slides | |
+| 1:40pm-2:30pm | Association Tests: Background | [Slides](https://drive.google.com/file/d/1AOCXrMpmUWErQt3BhXVM1ePGOJxvgruz/view?usp=drive_link) | |
+| 2:30pm-3:00pm | Getting Started with BioData Catalyst powered by Seven Bridges | [Slides](https://docs.google.com/presentation/d/1F5LznutVHVKirsvDFurh_S1aCbNHHQhCC5JPK_0_1EY/preview?slide=id.p) | |
+| 3:00pm-3:30pm | _Coffee Break_ | | |
+| 3:30pm-3:50pm | Intro to Cloud Computing for WGS Analyses | [Slides](https://docs.google.com/presentation/d/1qoDoRpUvMyPtB1Y-Z9CzBHbk2wDWtsloVvD_eNDy_Uc/preview?slide=id.p) | |
+| 3:50pm-5:00pm | Intro to Genomic Data Structure Format | [Slides](https://drive.google.com/file/d/1o2k1L5J961pTDNvLxlhK8cfmtUKDjuNl/view?usp=drive_link) | [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/01_gds_intro.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/01_gds_intro.html) |
+
+
+**Thursday, July 27th**
+
+| Time | Topic | Lecture | Exercises/Discussion |
+| --- | --- | --- | --- |
+| 8:30am-10:00am | Single Variant Association Tests | [Slides](https://drive.google.com/file/d/1AOCXrMpmUWErQt3BhXVM1ePGOJxvgruz/view?usp=drive_link) | [Slides](https://drive.google.com/file/d/1m2AT0qd04H1Z28qXlc9Miec2eGIZ22k6/view?usp=drive_link) [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/02_single_variant_tests.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/02_single_variant_tests.html) |
+| 10:00am-10:30am | _Coffee Break_ | | |
+| 10:30am-10:45am | Single Variant Association Tests (Discussion) | | |
+| 10:45am-12:00pm | Population Structure and Relatedness Inference for Association Studies | [Slides](https://drive.google.com/file/d/1rbcL7R3hut5OsEpB_e8Om1gdTXdQdGoJ/view?usp=drive_link) | [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/03_pop_structure_relatedness.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/03_pop_structure_relatedness.html) |
+| 12:00pm-1:30pm | _Lunch Break_ | | |
+| 1:30pm-1:45pm | Population Structure and Relatedness Inference (Discussion) | | |
+| 1:45pm-3:00pm | Mixed Model Association Tests | [Slides](https://drive.google.com/file/d/1stIM_xknIfJUJwUl3LMJo5zNaBxv5kpD/view?usp=drive_link) | [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/04_mixed_models.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/04_mixed_models.html) |
+| 3:00pm-3:30pm | _Coffee Break_ | | |
+| 3:30pm-4:00pm | Mixed Model Association Tests (Discussion) |
+| 4:00pm-4:45pm | R shiny Apps for Exploring Results Demo | | [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/05_exploring_association_results.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/05_exploring_association_results.html) |
+| 4:45pm-5:00pm | Open Q&A | | |
+
+**Friday, July 28th**
+
+| Time | Topic | Lecture | Exercises/Discussion |
+| --- | --- | --- | --- |
+| 8:30am-10:00am | Recent Findings and Resources for WGS Studies | [Slides](https://docs.google.com/presentation/d/1dwRILfGhTn5Yse2sP30zNLLir9RQLJKi/preview?pli=1&slide=id.p1) | |
+| 10:00am-10:30am | _Coffee Break_ | | |
+| 10:30am-12:00pm | Multiple Variant Association Tests | [Slides](https://drive.google.com/file/d/1AOCXrMpmUWErQt3BhXVM1ePGOJxvgruz/view?usp=drive_link) | [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/07_aggregate_tests.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/07_aggregate_tests.html) |
+| 12:00pm-1:30pm | _Lunch Break_ | | |
+| 1:30pm-2:00pm | Multiple Variant Association Tests (Discussion) | | |
+| 2:00pm-3:00pm | Variant Annotation & Annotation Explorer | Slides | [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/06_annotation_explorer.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/06_annotation_explorer.html) |
+| 3:00pm-3:30pm | _Coffee Break_ | | |
+| 3:30pm-4:30pm | Advanced Annotation Strategies for Association Testing & STAAR Pipeline | [Slides](https://docs.google.com/presentation/d/1Apc7JrJCvwei5iaCS8O5uX9j-UUIHM46/preview?slide=id.p1) | [.Rmd](https://github.com/UW-GAC/SISG_2023/blob/main/08_STAAR.Rmd) [.html](https://htmlpreview.github.io/?https://github.com/UW-GAC/SISG_2023/blob/main/08_STAAR.html) |
+| 4:30pm-5:00pm | Open Q&A | | |
+
+## R packages used
+
+- [GENESIS](http://bioconductor.org/packages/release/bioc/html/GENESIS.html)
+- [SeqArray](http://bioconductor.org/packages/release/bioc/html/SeqArray.html)
+- [SeqVarTools](http://bioconductor.org/packages/release/bioc/html/SeqVarTools.html)
+- [SNPRelate](http://bioconductor.org/packages/release/bioc/html/SNPRelate.html)
+- [Biobase](https://bioconductor.org/packages/release/bioc/html/Biobase.html)
+- [GGally](https://cran.r-project.org/web/packages/GGally)
+
+
+## Resources
+
+A detailed tutorial and relevant R scripts for STAAR pipeline are available at [https://github.com/xihaoli/STAARpipeline-Tutorial](https://github.com/xihaoli/STAARpipeline-Tutorial).
+
+If you are new to R, you might find the following material helpful:
+
+- [Introduction to R](http://faculty.washington.edu/kenrice/rintro/) materials from SISG Module 3
+- Graphics with [ggplot2](https://ggplot2.tidyverse.org/)
+- Data manipulation with [dplyr](http://dplyr.tidyverse.org/)