Explore the many useful functions that the Bioconductor environment offers for working with genomic data and other biological sequences.

DNA and proteins are often represented as files containing strings of nucleic acids or amino acids. They are associated with text files that provide additional contextual information such as genome annotations.

This workshop provides hands-on experience with tools, software and packages available in R via Bioconductor for manipulating, exploring and extracting information from biological sequences and annotation files. We will look at tools for working with some commonly used file formats including FASTA, GFF3, GTF, methods for identifying regions of interest, and easy methods for obtaining data packages such as genome assemblies.

Date/time: 10am-1pm AEST, Thursday 23 September 2021

Lead Trainer: Dr Paul Harrison, Monash Bioinformatics Platform

Learning outcomes

After attending this workshop, participants will be able to:

1. Work with data types in R representing DNA and amino-acid sequences, and genomic ranges (representing things such as genes, transcripts, exons, motif matches, or results of peak-calling).
2. Perform useful operations on genomic ranges such as finding overlaps between two sets of ranges.
3. Load and save data in commonly used file formats, appreciate some of the advantages and disadvantages of different formats.
4. Install Bioconductor packages, find relevant documentation, and be aware of differences between the Bioconductor and base R ways of doing things.

Who the workshop is for

This workshop is open to Australian students and researchers who are using Bioconductor to analyse their life science data. It is not suitable for absolute beginners.

Some familiarity with R is assumed (prospective participants should already be comfortable with basic R concepts).

Participants will need to have RStudio and R ready for use on their laptop.

Participants should have used a few Bioconductor packages, perhaps having worked through a tutorial vignette to perform a standard data analysis task. This workshop will assist those who are now interrogating their data in a way that requires going off the beaten path, or perhaps needing to better understand package vignettes mentioning things like "GRanges" and "TxDb".

How to apply

This workshop is free but participation is subject to application with selection. Applications close at 5pm AEST Thursday 9 Sep 2021.

You must be associated with an Australian organisation and provide an appropriate organisational email address for your application to be considered.

Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Monday 13 Sep 2021. Successful applicants will be provided with a Zoom meeting link closer to the date.

Apply here

This workshop is presented by the Australian BioCommons and Monash Bioinformatics Platform with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.

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