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index.Rmd
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---
output:
html_document:
theme: cosmo
---
## SISBID: Module 1 Accessing Biomedical Data
**Instructors:** [Raphael Gottardo](http://www.rglab.org/) and [Jeff Leek](http://www.jtleek.com/)
**Teaching assitants:** [Jean Morrison](http://students.washington.edu/jeanm5/) and [Brian Williamson](http://students.washington.edu/brianw26/)
**Class Schedule:**
* [Daily schedule](http://www.biostat.washington.edu/suminst/sisbid/schedule)
* [Location](http://www.biostat.washington.edu/suminst/sisbid/maps)
**Ressources:**
* [Rstudio](http://www.rstudio.com/), [R project](http://www.r-project.org/), and [Bioconductor](http://bioconductor.org/)
* [Rstudio's cheatsheets](http://www.rstudio.com/resources/cheatsheets/) & [Data.table cheatsheet](https://s3.amazonaws.com/assets.datacamp.com/img/blog/data+table+cheat+sheet.pdf)
**Getting Started:**
Please read this to setup your installation of R, git, and install required R packages
https://github.com/SISBID/Module1/blob/gh-pages/getting_started.md
**Schedule**
| Day | Date | Session | Resources | Description |
|---|---|---|---|---|
| 0 | 2015-06-15 | Background | [Try R](http://tryr.codeschool.com/) | Really simple intro to R online |
| 0 | 2015-06-15 | Background | [swirl](http://swirlstats.com/) | More tutorials on R, in R |
|1 | 2015-07-06 | 8:30AM - 10:00AM | [html slides](https://slides.com/jeffleek/sisbid-m1-d1) [pdf slides](https://dl.dropbox.com/s/kpf7yidry8ywkbf/sisbid-m1-d1.pdf) [labs](https://github.com/SISBID/Module1/tree/gh-pages/labs) | Welcome, motivation, installation |
|1 | --- | 10:00AM - 10:30AM | Break | --- |
|1 | 2015-07-06 | 10:30AM - 12:00PM | [html slides](https://slides.com/jeffleek/sisbid-m1-d1) [pdf slides](https://dl.dropbox.com/s/kpf7yidry8ywkbf/sisbid-m1-d1.pdf) [labs](https://github.com/SISBID/Module1/tree/gh-pages/labs) | Getting data |
|1 | --- | 1:30PM - 3:00PM | [html slides](lecture_notes/Bioconductor_intro.html) [md file](https://github.com/SISBID/Module1/blob/gh-pages/lecture_notes/Bioconductor_intro.md) | Intro to Bioconductor |
|1 | --- | 1:30PM - 3:00PM | [html slides](lecture_notes/data_manipulation_review.html) [md file](https://github.com/SISBID/Module1/blob/gh-pages/lecture_notes/data_manipulation_review.md) | Review of data.table and SQL |
|1 | --- | 3:00PM - 3:30PM | Break | --- |
|1 | --- | 3:30PM - 5:00PM | [html slides](lecture_notes/Bioconductor_intro.html) [md file](https://github.com/SISBID/Module1/blob/gh-pages/lecture_notes/Bioconductor_intro.md) | Intro to Bioconductor suite and use case |
|---|---|---|---|---|
|2 | 2015-07-06 | 8:30AM - 10:00AM | [html slides](https://slides.com/jeffleek/sisbid-m1-d2) [pdf slides](https://dl.dropbox.com/s/q29sspevqn3h2jk/sisbid-m1-d2.pdf) [labs](https://github.com/SISBID/Module1/tree/gh-pages/labs) | Cleaning data |
|2 | --- | 10:00AM - 10:30AM | Break | --- |
|2 | 2015-07-06 | 10:30AM - 12:00PM | [html slides](https://slides.com/jeffleek/sisbid-m1-d2) [pdf slides](https://dl.dropbox.com/s/q29sspevqn3h2jk/sisbid-m1-d2.pdf) [labs](https://github.com/SISBID/Module1/tree/gh-pages/labs) | Cleaning data |
|2 | 2015-07-07 | 1:30PM - 3:00PM | [html slides](lecture_notes/Lab_Searching_GEO.html) [md file](https://github.com/SISBID/Module1/blob/gh-pages/lecture_notes/Lab_Searching_GEO.md) | Lab time (GEO and more) |
|2 | 2015-07-07 | 3:00PM - 3:30PM | Break | Break |
|2 | --- | 3:30PM - 5:00PM | [html slides](lecture_notes/Lab_Searching_GEO.html) [md file](https://github.com/SISBID/Module1/blob/gh-pages/lecture_notes/Lab_Searching_GEO.md) | Lab time (GEO and more) |
|---|---|---|---|---|
|3 | --- | 10:30PM - 12:00PM | [html slides](lecture_notes/ImmuneSpaceR_lab.html) [md file](https://github.com/SISBID/Module1/blob/gh-pages/lecture_notes/ImmuneSpaceR_lab.md) | Lab time on ImmuneSpace |
**NOTE:** The md files linked in the table above can easily be converted to pdf by replacing *github* by *gitprint* in the url (when opening the link in your web browser)
<!-- Add links to the rest of the material as we go
-->
**Miscellaneous**
Feel free to submit typos/errors/etc via the github repository associated with the class:
https://github.com/SISBID/Module1
This web-page is modified from Andrew Jaffe's [Summer 2015 R course](http://www.aejaffe.com/summerR_2015/), which also has great material (some overlapping with ours).
```{r, eval = FALSE, echo = FALSE}
## Render this file:
rmarkdown::render('index.Rmd')
```
This page was last updated on `r Sys.time()` Eastern Time.