Working with DNA sequences and features in R with Bioconductor - version 2

Workshop material

• Slides
• Workshop

Setup

Download and install:

• R
• RStudio
• IGV (optional)

We recommend creating a new “project” in RStudio for this workshop. This will ensure you are working in a fresh working directory. Once you have opened the project, copy and paste the following code to the R console to download necessary files and install packages. During the workshop we will be working through the code in the file “workshop.R”.

# Download files for workshop
filenames <- c(
    "workshop.R", 
    "Caenorhabditis_elegans.WBcel235.104.gtf.gz", 
    "Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa.gz",
    "example.bam",
    "example.bam.bai")

for(filename in filenames) {
    download.file(
        paste0("https://monashdatafluency.github.io/r-bioc-2/", filename),
        filename)
}

# Install packages used in workshop
install.packages("BiocManager")
BiocManager::install(c(
    "Biostrings",
    "BSgenome",
    "GenomicRanges",
    "GenomicFeatures",
    "ensembldb",
    "rtracklayer",
    "Rsamtools",
    "Gviz",
    "seqLogo",
    "org.Ce.eg.db",
    "GO.db",
    "biomaRt",
    "AnnotationHub"))


# Worm FASTA and GTF files are originally from:
# http://ftp.ensembl.org/pub/release-104/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa.gz
# http://ftp.ensembl.org/pub/release-104/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.104.gtf.gz

Further reading

• Most of the packages used in this workshop have useful vignettes.

• There are workflow tutorials with step-by-step instructions for specific analysis tasks.

• The file format FAQ by UCSC. Mentioned in this workshop are GTF, GFF, BAM, bigWig. Also see FASTA for sequences. samtools and related tools can make an index for many of these file types, for fast access by genome browsers and other software.

• The plyranges package by Stuart Lee provides a “tidy” approach to GRanges. Stuart has also written an introduction to S4 classes.

• Mike Love’s Bioconductor reference card has many useful code snippets.

• James MacDonald and Lori Sheppard gave an introduction to Bioconductor annotation resources at Bioc2021: video, workshop material. Includes discussion of Bioconductor’s history.

• Course materials and videos are regularly added to the Bioconductor site.

• Ask questions on the support site. (Remember to check if your question has already been answered.)

Author

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

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

Source code

• GitHub repository