index.Rmd

---
title: "Statistical Analysis of Genome Scale Data 2023"
author: "Leonardo Collado-Torres"
site: bookdown::bookdown_site
apple-touch-sin: "icon_192.png"
apple-touch-icon-size: 192
favicon: "icon_32.png"
github-repo: "lcolladotor/cshl_rstats_genome_scale_2023"
documentclass: book
output:
  bookdown::gitbook:
    includes:
      after_body: map_and_ga.html
    css: "style.css"
    
---

# Overview {-}

Here you can find the files for the July 2023 _Statistical Analysis of Genome Scale Data_ course at [CSHL](https://meetings.cshl.edu/courses.aspx?course=C-DATA&year=23) portion taught by Leo and his team (July 3rd to July 6th). See [CSHLData2023](https://seandavi.github.io/CSHLData2023/) for a list of all instructors and related materials.

Instructor:

* [**Leonardo Collado-Torres**](http://lcolladotor.github.io/), [Twitter](https://twitter.com/lcolladotor)

Teach assistants:

* [Daianna González Padilla](https://daianna21.github.io/), [Twitter](https://twitter.com/daianna_glez)
* [Fernanda Renee García Flores](https://reneegf.github.io/), [Twitter](https://twitter.com/SubmarineGene)

<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Happy to welcome <a href="https://twitter.com/lcolladotor?ref_src=twsrc%5Etfw">@lcolladotor</a>, <a href="https://twitter.com/SubmarineGene?ref_src=twsrc%5Etfw">@SubmarineGene</a>, and <a href="https://twitter.com/daianna_glez?ref_src=twsrc%5Etfw">@daianna_glez</a> to <a href="https://twitter.com/cshlcourses?ref_src=twsrc%5Etfw">@cshlcourses</a> on Statistical Analysis of Genome Scale Data. Materials here:<a href="https://t.co/0JGzEEf3Yx">https://t.co/0JGzEEf3Yx</a></p>&mdash; Sean Davis (@seandavis12) <a href="https://twitter.com/seandavis12/status/1675926879826485253?ref_src=twsrc%5Etfw">July 3, 2023</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Interested in learning R/<a href="https://twitter.com/Bioconductor?ref_src=twsrc%5Etfw">@Bioconductor</a> for <a href="https://twitter.com/hashtag/RNAseq?src=hash&amp;ref_src=twsrc%5Etfw">#RNAseq</a> data analysis?<br><br>Check <a href="https://t.co/jcNWOq7VWD">https://t.co/jcNWOq7VWD</a> that <a href="https://twitter.com/daianna_glez?ref_src=twsrc%5Etfw">@daianna_glez</a> <a href="https://twitter.com/SubmarineGene?ref_src=twsrc%5Etfw">@SubmarineGene</a> and I built for a CSHL course organized by <a href="https://twitter.com/seandavis12?ref_src=twsrc%5Etfw">@seandavis12</a> &amp; Vincent Carey<a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a> <a href="https://twitter.com/LieberInstitute?ref_src=twsrc%5Etfw">@LieberInstitute</a> <a href="https://twitter.com/cshlcourses?ref_src=twsrc%5Etfw">@cshlcourses</a> <br><br>Source at <a href="https://t.co/aQ8kLMadSl">https://t.co/aQ8kLMadSl</a> ⭐️</p>&mdash; 🇲🇽 Leonardo Collado-Torres (@lcolladotor) <a href="https://twitter.com/lcolladotor/status/1678488349307461632?ref_src=twsrc%5Etfw">July 10, 2023</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

## Download course materials {-}

Download the materials for this course with `usethis::use_course('lcolladotor/cshl_rstats_genome_scale_2023')` or view online at [**lcolladotor.github.io/cshl_rstats_genome_scale_2023**](http://lcolladotor.github.io/cshl_rstats_genome_scale_2023). This command downloads a static version of the course materials. 

If you want to be able to easily download updates, we recommend using `Git`. [_Happy Git and GitHub for the useR_](https://happygitwithr.com/) is great for getting your computer ready to use `Git` and `GitHub`. If you already have a `GitHub` account, you can instead use this command to download the course:

```bash
## Download it the first time
git clone https://github.com/lcolladotor/cshl_rstats_genome_scale_2023.git

## To update the contents, use:
cd cshl_rstats_genome_scale_2023
git pull
```

Or you could use the [GitHub Desktop application](x-github-client://openRepo/https://github.com/lcolladotor/cshl_rstats_genome_scale_2023).

## Code of Conduct {-}

We'll follow the CSHL code of conduct as well as version 1.2.0 of the Bioconductor code of conduct [bioconductor.github.io/bioc_coc_multilingual/](https://bioconductor.github.io/bioc_coc_multilingual/). 

For reporting any violations of the code of conduct, report them to the Instructor and/or Course Coordinators.

## Course Schedule {-}

_Local times in US Eastern_

See [CSHLData2023](https://docs.google.com/document/d/1pdvZFjJBwRUpA_VJOAFu4z-0Eys6Wv2iRAh84T6_yF4/edit?usp=sharing) for the detailed schedule. Below is a list of the key packages we will use each day:

* Monday July 3rd: `SummarizedExperiment`, `iSEE`, `smokingMouse`, `biocthis`
* Tuesday July 4th: `recount3`, `ExploreModelMatrix`, `limma`
* Wednesday July 5th: `variancePartition`, `ComplexHeatmap`
* Thursday July 6th: `spatialLIBD`
  
## External links {-}

* [CSHL course](https://meetings.cshl.edu/courses.aspx?course=C-DATA&year=23)
* [CSHLData2023](https://seandavi.github.io/CSHLData2023/)
* [GitHub source code](https://github.com/lcolladotor/cshl_rstats_genome_scale_2023)
* [Slack](https://cshldata-2023.slack.com)
* Example real project (by Daianna): [LieberInstitute/smokingMouse_Indirects](https://github.com/LieberInstitute/smokingMouse_Indirects)
* `SPEAQeasyWorkshop2023` for BioC2023 (by Daianna and Renee): [LieberInstitute/SPEAQeasyWorkshop2023](https://github.com/LieberInstitute/SPEAQeasyWorkshop2023)
* [LieberInstitute/template_project](https://github.com/LieberInstitute/template_project)
* [LIBD rstats club](http://research.libd.org/rstatsclub/): check the [public schedule](https://docs.google.com/spreadsheets/d/1is8dZSd0FZ9Qi1Zvq1uRhm-P1McnJRd_zxdAfCRoMfA/edit?usp=sharing)
  

## Course Prerequisites {-}

Install R 4.3.x from [CRAN](https://cran.r-project.org/) then install the following R packages:

```{r install, eval = FALSE}
## For installing Bioconductor packages
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

## Install required packages
BiocManager::install(
    c(
        "usethis", ## Utilities
        "BiocFileCache",
        "RefManageR",
        "here",
        "Hmisc",
        "biocthis",
        "lobstr",
        "postcards",
        "scater",
        "sessioninfo",
        "smokingMouse",
        "stringr",
        "SummarizedExperiment", ## Main containers / vis
        "iSEE",
        "edgeR", ## RNA-seq
        "ExploreModelMatrix",
        "limma",
        "recount3",
        "rlang",
        "pheatmap", ## Visualization
        "ggplot2",
        "ggrepel",
        "patchwork",
        "RColorBrewer",
        "ComplexHeatmap",
        "cowplot",
        "Polychrome",
        "spatialLIBD", ## Advanced
        "variancePartition"
    )
)

## Install smokingMouse, which is currently under review at Bioconductor
## at https://github.com/Bioconductor/Contributions/issues/3024.
BiocManager::install("LieberInstitute/smokingMouse")

## Required to access some recent bug fixes on biocthis
BiocManager::install("lcolladotor/biocthis")
```

You will also need to install [RStudio](https://rstudio.com/products/rstudio/download/#download) version 2023.06.0+421 or newer.

## R session information {-}

Details on the R version used for making this book. The source code is available at [`lcolladotor/cshl_rstats_genome_scale_2023`](https://github.com/lcolladotor/cshl_rstats_genome_scale_2023).

```{r session_packages, eval = TRUE, message = FALSE}
## Load the package at the top of your script
library("sessioninfo")

## Utilities
library("BiocFileCache")
library("BiocStyle")
library("biocthis")
library("here")
library("lobstr")
library("postcards")
library("usethis")
library("sessioninfo")

## Data
library("smokingMouse")

## Main containers / vis
library("SummarizedExperiment")
library("iSEE")

## RNA-seq
library("edgeR")
library("ExploreModelMatrix")
library("limma")
library("recount3")

## QCA
library("scater")

## Variance Partition
library("variancePartition")

## Visualization: plots & text
library("ComplexHeatmap")
library("ggplot2")
library("patchwork")
library("pheatmap")
library("RColorBrewer")
library("Hmisc")
library("stringr")
library("cowplot")
library("rlang")
library("ggrepel")
library("Polychrome")

## Spatial transcriptomics
library("spatialLIBD")
```

```{r session_info}
## Reproducibility information
options(width = 120)
session_info()
proc.time()
```

This interactive book was last updated at `r Sys.time()`.

## License  {-}

<a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc-sa/4.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>.