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Workshop material

Setup

This workshop is best done using RStudio and R on your laptop. We recommend you create a new project to contain the files. Alternatively you can use RStudio Cloud over the web (Monash users can log in with their Monash google account).

Optionally, also download and install IGV 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.

# 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:

Author

This course has been developed for the Monash Bioinformatics Platform and Monash Data Fluency by Paul Harrison.

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.

Source code