ShortCourse_2023

ShortCourse_2023/00_prerequisites/00a_General_Installation_Requirements.md

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+# Addiction ShortCourse 2018 - Prerequisites
+
+## Downloading and Installation of Software and Programming enviornments
+
+### R and RStudio
+Please ensure you have the latest version of R and RStudio installed on your machine. This is important, as some packages used in the workshop may not install correctly (or at all) if R is not up to date.
+
+Download and install the latest version of R - [download link](http://cran.stat.ucla.edu/)
+
+Download and install RStudio - [download link](https://www.rstudio.com/products/rstudio/download/#download)
+
+### Jupyter Notebook
+
+#### Installing Jupyter using Anaconda
+The Jupyter Notebook Developers strongly recommend installing Python and Jupyter using the Anaconda Distribution, which includes Python, the Jupyter Notebook, and other commonly used packages for scientific computing and data science.
+
+Step 1: Download Anaconda. We recommend downloading Anaconda’s latest Python 3 version.
+
+  For macOS - [here](https://www.anaconda.com/download/#macos)
+  For Windows - [here](https://www.anaconda.com/download/#windows)
+
+Step 2: Install the version **Python 3.6 version**, following the instructions on the download page.
+
+Step 3: Launch Anaconda-Navigator
+
+Step 4: From the Anaconda-Navigator UI click on the "Launch" button associated with Jupyter Notebooks (highligthed in green)
+![](../imgs/Anaconda-Navigator-UI.png)
+
+### Python
+The installation of Jupyter Notebook takes care of the installation of Python and therefore we do not need to install Python separately.
+
+
+
+
+

ShortCourse_2023/00_prerequisites/00b_Introduction_to_RStudio.md

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+# Introduction to RStudio
+
+For those who are new to Rstudio, it would be good to take a few minutes to orient yourself to Rstudio. In addition to this, it would be could to see how to excute R commands in Rstudio. For this, we will make use of the lessons provided by the [Software Carperntry Organization](https://software-carpentry.org/). They have made avialble several short lessons to become comfortable with Rstudio and R [here](https://swcarpentry.github.io/r-novice-gapminder/). We are specifically interested in the [**Introduction to R and RStudio**](https://swcarpentry.github.io/r-novice-gapminder/01-rstudio-intro/index.html) lesson.

ShortCourse_2023/00_prerequisites/01_02_Prerequisites for the Reproducibility and Accessing Mouse Resources Modules.md

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+
+Installation of Jupyter Notebooks and Python, which come bundled with Anaconda Navigator are the only prerequisites. If you have already installed these, then please ignore the section below.
+
+### Jupyter Notebook
+
+#### Installing Jupyter using Anaconda
+The Jupyter Notebook Developers strongly recommend installing Python and Jupyter using the Anaconda Distribution, which includes Python, the Jupyter Notebook, and other commonly used packages for scientific computing and data science.
+
+Step 1: Download Anaconda. We recommend downloading Anaconda’s latest Python 3 version.
+
+  For macOS - [here](https://www.anaconda.com/download/#macos)
+  For Windows - [here](https://www.anaconda.com/download/#windows)
+
+Step 2: Install the version **Python 3.6 version**, following the instructions on the download page.
+
+Step 3: Launch Anaconda-Navigator
+
+Step 4: From the Anaconda-Navigator UI click on the "Launch" button associated with Jupyter Notebooks (highligthed in green)
+![](../imgs/Anaconda-Navigator-UI.png)
+
+### Python
+The installation of Jupyter Notebook takes care of the installation of Python and therefore we do not need to install Python separately.

ShortCourse_2023/00_prerequisites/03_04_Prerequisites for the Gene Expression and QTL Mapping Modules.md

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+
+# Installation of required R packages
+
+The following R packages are required for the successful completion of the following workshop modules: 
+
+1. Gene Expression 
+
+2. QTL Mapping
+
+Most of the packages will be installed using BiocManager. Our first step therefore is to install BiocManager (<https://bioconductor.org/install>),
+
+## Install BiocManager
+
+```         
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+BiocManager::install()
+```
+
+## Gene Expression
+
+In the gene expression module we will be undertaking a differential gene expression analysis. For this, we will make use of the [DESeq2](https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html) R package. To install this package, copy and paste the commands below in your R console:
+
+```         
+BiocManager::install("DESeq2")
+```
+
+In addition to DESeq2 we will need the following R packages as well:
+
+### libraries for gene expression analysis
+
+```         
+BiocManager::install("vsn", force = TRUE)
+```
+
+### libraries for table manipulations
+
+```         
+BiocManager::install("DT", force = TRUE)
+BiocManager::install("plyr", force = TRUE)
+```
+
+### libraries for visualization
+
+```         
+BiocManager::install("ggplot2", force = TRUE)
+BiocManager::install("pheatmap", force = TRUE)
+BiocManager::install("RColorBrewer", force = TRUE)
+```
+
+###libraries for gene annotation and enrichement analysis
+
+```         
+BiocManager::install("org.Mm.eg.db", force = TRUE)
+BiocManager::install("topGO", force = TRUE)
+```
+
+## QTL Mapping
+
+QTL mapping workshop will require the installation of the following R libraries. Copy and paste the commands below in you R console:
+
+```         
+BiocManager::install("qtl2", force = TRUE)
+BiocManager::install("GGally", force = TRUE)
+```
+
+# External datasets that need to be downloaded
+
+The QTL mapping workshop, particularly the one on Diversity Outbred mice, has a section on **SNP Association Mapping** that requires the following two files:
+
+-   cc_variants.sqlite [Download here](https://doi.org/10.6084/m9.figshare.5280229.v2) : These are the variants in the Collaborative Cross founders (3 GB)
+-   mouse_genes.sqlite [Download here](https://doi.org/10.6084/m9.figshare.5280238.v4) : full set of mouse gene annotations (677 MB)

ShortCourse_2023/00_prerequisites/05_Prerequisites for the GWAS Module.md

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+
+# Recent methods for polygenic analysis of genome-wide data
+
+## Primary objective
+The primary objective of this module is to:
+- Estimate SNP-heritability
+- Calculate genetic correlations
+- Perform functional mapping and annotation of genetic associations
+
+
+
+## Dataset and tools
+The datasets and tools that will be used in the workshop will leverage publicly avialable resources
+
+- Summary statistics (PGC, GWAS catalog):
+  - https://www.med.unc.edu/pgc/results-and-downloads
+  - https://www.ebi.ac.uk/gwas/downloads/summary-statistics
+
+- SNP-heritability and genetic correlations (LDHub):
+  - http://ldsc.broadinstitute.org/ldhub/
+![](../imgs/LDHub.png)
+
+**You will need to login in to LDHub using your gmail account**
+
+- Functional annotation (FUMA):
+  - http://fuma.ctglab.nl/login
+![](../imgs/fuma_signup.png)
+
+**You will need to create an user account to use FUMA**
+
+However, if for some reason there are difficulties in doing so we have created the following account:
+
+- account: [email protected]; password: jaxpolygenicity2018
+

ShortCourse_2023/00_prerequisites/06_Prerequisites for the CRISPR Module.md

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+
+# Workshop on Guide Design
+The primary objective of this workshop is in understanding the nuances of CRISPR Guide Design and to produce a CRISPR design for point mutation. To do this we will make use of the OPRM1 example from [Kringel et al.](https://www.nature.com/articles/tpj201628); [alternate link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5637232/)
+
+
+# Create a Benchling Account
+This workshop uses the tool **Benchling**. Please make sure to create a free account [here](https://benchling.com/signup), prior to the start of this workshop. The signup button is on the top right hand corner of the page.
+![](../imgs/benchling_signup.png)

ShortCourse_2023/01_Reproducibility_and_Traceability/01_02_Prerequisites for the Reproducibility and Accessing Mouse Resources Modules.md

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+
+Installation of Jupyter Notebooks and Python, which come bundled with Anaconda Navigator are the only prerequisites. If you have already installed these, then please ignore the section below.
+
+### Jupyter Notebook
+
+#### Installing Jupyter using Anaconda
+The Jupyter Notebook Developers strongly recommend installing Python and Jupyter using the Anaconda Distribution, which includes Python, the Jupyter Notebook, and other commonly used packages for scientific computing and data science.
+
+Step 1: Download Anaconda. We recommend downloading Anaconda’s latest Python 3 version.
+
+  For macOS - [here](https://www.anaconda.com/download/#macos)
+  For Windows - [here](https://www.anaconda.com/download/#windows)
+
+Step 2: Install the version **Python 3.6 version**, following the instructions on the download page.
+
+Step 3: Launch Anaconda-Navigator
+
+Step 4: From the Anaconda-Navigator UI click on the "Launch" button associated with Jupyter Notebooks (highligthed in green)
+![](../imgs/Anaconda-Navigator-UI.png)
+
+### Python
+The installation of Jupyter Notebook takes care of the installation of Python and therefore we do not need to install Python separately.

ShortCourse_2023/02_Accessing_Mouse_Data_Resources/01_02_Prerequisites for the Reproducibility and Accessing Mouse Resources Modules.md

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+---
+output:
+  pdf_document: default
+  html_document: default
+---
+
+Installation of Jupyter Notebooks and Python, which come bundled with Anaconda Navigator are the only prerequisites. If you have already installed these, then please ignore the section below.
+
+### Jupyter Notebook
+
+#### Installing Jupyter using Anaconda
+The Jupyter Notebook Developers strongly recommend installing Python and Jupyter using the Anaconda Distribution, which includes Python, the Jupyter Notebook, and other commonly used packages for scientific computing and data science.
+
+Step 1: Download Anaconda. We recommend downloading Anaconda’s latest Python 3 version.
+
+  For macOS - [here](https://www.anaconda.com/download/#macos)
+  For Windows - [here](https://www.anaconda.com/download/#windows)
+
+Step 2: Install the version **Python 3.6 version**, following the instructions on the download page.
+
+Step 3: Launch Anaconda-Navigator
+
+Step 4: From the Anaconda-Navigator UI click on the "Launch" button associated with Jupyter Notebooks (highligthed in green)
+![](../imgs/Anaconda-Navigator-UI.png)
+
+### Python
+The installation of Jupyter Notebook takes care of the installation of Python and therefore we do not need to install Python separately.