This is a QCIF course and places are highly limited as Graduate School is paying the fee. If you are unable to attend, please de-register (or email graduateschool@uq.edu.au if you are unable to do so). An unexplained absence could result in all your future QCIF registrations becoming Waitlisted.

Galaxy Australia is a platform that provides a simple and user-friendly interface to bioinformatics tools. The output we will generate is suitable for further analysis within Galaxy Australia, or locally.

Recommended Participants

Life scientists planning or running single cell RNAseq experiments (or mining public data), who want to perform their own analyses. All analysis is performed via the web browser.  

Participants should have a basic understanding of single cell RNAseq technology. No bioinformatics, programming, command line or single cell RNAseq analysis experience is expected. Previous experience using Galaxy is helpful but not required.

Learning Objectives

  • Understand the steps required in a typical single-cell RNA-Seq analysis
  • Determine and apply appropriate QC thresholds
  • Take a counts matrix, apply filtering, run UMAP and plot the results
  • Generate cell clusters and identify marker genes for cell type identification
  • Run a basic differential expression analysis
  • Understand the iterative nature of single-cell RNA-Seq analysis
  • Understand how single-cell RNA-Seq data and annotations can be saved in AnnData format and shared

Syllabus

  • Introduction to single-cell RNA-Seq analysis and Galaxy
  • QC and filter a counts matrix
  • Reduce dimensionality: PCA and UMAP 
  • Clustering
  • Basic differential expression
  • Plotting and visualisations
  • Options for further analysis

About Bioinformatics and genomics

If your research study involves bioinformatics and genomics, we've got you covered! The Graduate School works with different providers to provide a range of sessions with esteemed providers such as QCIF.

Useful links

  • Queensland Facility for Advanced Bioinformatics (QFAB): Bioinformatics, biostatistics and biodata expertise
  • Hacky Hour (supported by RCC, QCIF, IMB and wonderful volunteer helpers!): RCC runs consultations every Tuesday at Cafe Nano. Come and ask IT questions such as: getting started with Python and R, stats, machine learning, bio-image, software tools, research data management (RDM), how to access high performance computing, cloud data storage and tools for data cleaning and data visualisation. Bring your project's IT problems or come along as a helper! Very occasionally Hacky Hour may not run; follow us on Twitter (@HackyHourStLuc​) to get the latest announcements. Aside from the usual IT research questions, 
    • First Tuesday of the monthBioinformatics Hacky Hour, ask bioinformatics analysis, software and pipeline questions
    • Last Tuesday of the monthBioLab Hacky Hour, ask about experimental design and technical sample processing questions to get started in the lab