index.Rmd

---
title: "Intro RNA-seq LCG-UNAM 2021"
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/rnaseq_LCG-UNAM_2021"
documentclass: book
output:
  bookdown::gitbook:
    includes:
      after_body: map_and_ga.html
    css: "style.css"
    
---

# Overview {-}

Here you can find the files for the February 2021 introduction to R, RStudio and RNA-sequencing (RNA-seq) course for [LCG-UNAM](https://lcg.unam.mx/) at [CCG-UNAM](https://ccg.unam.mx/) (February 23-26, 2021). The rest of the chapters will be in Spanish.

Instructor:

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

Teach assistants:

* [Elisa Márquez Zavala](https://github.com/emarquezz)
* [Citlali Gil](https://github.com/CitlaliGA)


Course Coordinators:

* Heladia Salgado
* Julio Collado Vides

Download the materials for this course with `usethis::use_course('lcolladotor/rnaseq_LCG-UNAM_2021')` or view online at [**lcolladotor.github.io/rnaseq_LCG-UNAM_2021**](http://lcolladotor.github.io/rnaseq_LCG-UNAM_2021).

## Code of Conduct {-}

We'll follow the CDSB code of conduct [comunidadbioinfo.github.io/codigo-de-conducta/](https://comunidadbioinfo.github.io/codigo-de-conducta/) as well as version 1.0.1 of the Bioconductor code of conduct [bioconductor.org/about/code-of-conduct/](http://bioconductor.org/about/code-of-conduct/). 

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

## Course Schedule {-}

_Local times in Cuernavaca, Mexico_

* Tuesday February 23:
  - 9-11 am: introduction to R, RStudio, `r BiocStyle::CRANpkg("usethis")` and `r BiocStyle::CRANpkg("here")`
  - 12-2 pm: introduction to Bioconductor
* Wednesday February 24:
  - 9-11 am: expression data R/Bioconductor objects and visualization: `r BiocStyle::Biocpkg("SummarizedExperiment")` and `r BiocStyle::Biocpkg("iSEE")`
  - 12-2 pm: Downloading RNA-seq data using `r BiocStyle::Biocpkg("recount3")`
* Thursday February 25:
  - 9-11 am: statistical models with `r BiocStyle::Biocpkg("ExploreModelMatrix")`
  - 12-2 pm: differential expression analysis with `r BiocStyle::Biocpkg("limma")`
* Friday February 26:
  - 9-11 am: Review session
  - 12-2 pm: spatial transcriptomics with `r BiocStyle::Biocpkg("spatialLIBD")` + open discussion (career paths, networking, etc)
  
## External links {-}

* [Cursos LCG](https://cursos.lcg.unam.mx/mod/url/view.php?id=2220)
* [GitHub source code](https://github.com/lcolladotor/rnaseq_LCG-UNAM_2021)
* Zoom (ask)
* [LCG-UNAM RStudio server](http://132.248.220.108:8787/)
* [CDSB](https://comunidadbioinfo.github.io/)
* [Slack CDSB Mexico](https://comunidadbioinfo.slack.com)
  

## Course Prerequisites {-}

Install R 4.0.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
        "here",
        "biocthis",
        "postcards",
        "pryr",
        "sessioninfo",

        "SummarizedExperiment", ## Main containers / vis
        "iSEE",

        "edgeR", ## RNA-seq
        "ExploreModelMatrix",
        "limma",
        "recount3",

        "pheatmap", ## Visualization
        "ggplot2",
        "patchwork",
        "RColorBrewer",

        "spatialLIBD" ## Advanced
    )
)
```

You will also need to install [RStudio](https://rstudio.com/products/rstudio/download/#download) version 1.4 or newer.

## Course Evaluation {-}

* Participation
  - (main evidence) written and/or verbal participation during sessions and break-out rooms
  - (optional, strongly encouraged for your own career) Community building: CDSB Slack (introduce yourself), twitter, GitHub, etc.
* Public work
  - (main evidence) Taking notes on GitHub
  - (optional) Deploy an iSEE `shiny` app on shinyapps.io
  - (advanced and optional) R package with notes following `usethis::create_package()` + `biocthis::use_bioc_pkg_templates()`.
* Final project
  - (main evidence) code in a public URL (gist, GitHub, ...)
  - (optional) a rendered Rmd file (RPubs, GitHub)
  - (optional advanced) Copy this repository, remove all the Rmds except the index.Rmd and edit accordingly. GitHub Actions will then help you render it. You'll need to fetch the `gh-pages` branch and at least make one commit for the HTML to be available such as this [commit](https://github.com/lcolladotor/rnaseq_LCG-UNAM_2021/commit/e15bd6c234dd0ca4233050a4a0a42184994fef3b).
  
The final grade will be a weighted average from the student's self evaluation (10%), the evaluation by each TA (15% each), your participation as evaluated by the instructor (10%), your public work (20%) and your final project (30%).

Projects, public work and notes are due at 9 am US Eastern on Monday March 1st, though we recommend doing any work related to this course by Friday February 26th.

## R session information {-}

Details on the R version used for making this book. The source code is available at [`lcolladotor/rnaseq_LCG-UNAM_2021`](https://github.com/lcolladotor/rnaseq_LCG-UNAM_2021).

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

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

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

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

## Visualization
library("ggplot2")
library("patchwork")
library("pheatmap")
library("RColorBrewer")

## Advanced
library("spatialLIBD")
```

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

This 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>.