University of St. Andrews x Nygen - Accelerated Single Cell Data Analysis Course

‍Why this course?

This comprehensive single-cell RNA-Seq and multi-omics analysis course is designed to deliver actionable insights in a fraction of the time other multi-day workshops require.

Who is this for?

This course is ideal for PhD students, experimental researchers, bioinformaticians, and anyone looking to gain fluency in single-cell transcriptomics and multi omics research.

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Course outline:‍

Part 1 (No UMAPs yet)

000-005 - Intro

005-020 - Single-cell RNA-Seq Data Journey

020-035 - Data upload on Nygen

030-055 - Analysis setup and best practices

055-065 BREAK (Q&A session open)

Part 2 (UMAPs and beyond)

065-075: Data eploration: UMAPs, clusters

075-085: Data quality, batch effect

085-095: Cell type annotation

090-105: Cell selections and diff. gene. ep.

105-115: Publishing data

115-120: Wrap-up

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Learning Outcomes

- Process single-cell RNA-seq data from raw reads to biologically interpretable results

- Select appropriate analysis methods and tools (Seurat, Bioconductor, Scanpy, or Nygen)

- Interpret quality control metrics, clustering outputs, and differential expression results

- Integrate multiple datasets and correct for batch effects

- Annotate your data confidently to uncover meaningful biological insights