part0_prep.qmd

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title: "Preparation"
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Here are some preparation information for the participants.

## Software

In this workshop we will be using R. You can either

-   have **R and Rstudio** installed on your laptop
-   or, use **Posit cloud** (formerly Rstudio Cloud).

[Posit cloud](https://posit.cloud) is free of charge for personal users, yet you need to [sign up](https://posit.cloud/plans/free) for a new user account and have internet connection. Use this Posit cloud project: <https://posit.cloud/content/5131383>.

**Note:** In the Posit cloud project, all required R code and data sets should already be available, and all required R packages are already installed. If you plan to use your own laptop and local RStudio setup, then you will need to download the data and R code and install

## Required R packages

The R package we are using is `glmnet`. Otherwise, we use base R packages which are already installed by default. We will also need R package `gclus` for one of the tasks (not essential for running other parts of the lab). You can install the packages by running the following code:

```         
install.packages("glmnet")
install.packages("gclus")
```

## Data

The datasets we use can be found [here](https://github.com/ocbe-uio/2022_bioinformatics_workshop/tree/main/lab/data).

## Code

The R scripts used in part 1 and part 2 can be found [here](https://github.com/ocbe-uio/2022_bioinformatics_workshop/tree/main/lab/code).

## Resources

Lecture notes [link](https://github.com/ocbe-uio/2022_bioinformatics_workshop/tree/main/lecture_notes)

Lab notes [link](https://github.com/ocbe-uio/2022_bioinformatics_workshop/blob/main/lab/StatPrinciples_RLab.pdf)

Aure 2015 Paper [link](https://github.com/ocbe-uio/2022_bioinformatics_workshop/blob/main/lab/Aure_2015.pdf)