index.Rmd

---
title: "Working with DNA sequences and features in R with Bioconductor"
output: 
    html_document:
        theme: cerulean
        css: style.css
---

<div style="font-size: 150%">
<br>

This is the old version of this workshop.

[&rarr; Here is the new version.](https://monashdatafluency.github.io/r-bioc-2/)
</div>

## Workshop material

* [Slideshow](slides/slides.html)
* [Workshop](topics/sequences_and_features.html)

## Setup

This workshop is best done using [RStudio](https://rstudio.com/products/rstudio/download/) and [R](https://cran.r-project.org/) on your laptop. We recommend you create a new project to contain the files. Alternatively you can use [RStudio Cloud](https://rstudio.cloud/) over the web (Monash users can log in with their Monash google account). 

Optionally, also [download and install IGV](https://software.broadinstitute.org/software/igv/download) on your computer.

Once you've created a new project in RStudio, running the R code below will download files and install packages used in this workshop.

```{r eval=FALSE}
# Download data
download.file(
  "https://monashdatafluency.github.io/r-bioc/r-bioc-files.zip",
  destfile="r-bioc-files.zip")
unzip("r-bioc-files.zip")

# Install BiocManager package from CRAN:
install.packages("BiocManager")

# Install some Bioconductor packages:
BiocManager::install(c(
    "Biostrings", 
    "BSgenome", 
    "GenomicRanges", 
    "GenomicFeatures", 
    "ensembldb", 
    "rtracklayer", 
    "seqLogo", 
    "AnnotationHub"
), INSTALL_opts="--no-byte-compile")
```


## Workshop files

The above code will download and unzip the files for this workshop. You can also download them from:

* [r-bioc-files.zip](r-bioc-files.zip)


## Author

This course has been developed for the [Monash Bioinformatics Platform](https://www.monash.edu/researchinfrastructure/bioinformatics) and [Monash Data Fluency](https://www.monash.edu/data-fluency) by Paul Harrison.

<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="figures/CC-BY.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.

## Source code

* [GitHub repository](https://github.com/MonashDataFluency/r-bioc)

<p style="margin-top: 5em; text-align: right">
<a href="https://www.monash.edu/researchinfrastructure/bioinformatics"><img src="figures/MBP-banner.png" width="675"></a>
</p>