single-cell RNA

Single-Cell RNA-Seq & Multi Omics Data Analysis

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

Course formats & schedule

1. On-site Workshop

The session will be managed and hosted by you at your facility.

  • Dates & Location: Flexible: contact us to schedule your event.
  • Format: Deeper, hands-on modules (including Bring Your Own Data), face-to-face interaction, and personalized troubleshooting.

Note: On-site course will be limited to 30 participants per session (online or onsite) to ensure personalized attention and high-quality interaction.

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2. Online Intensive

  • Dates: Flexible: contact us to schedule your event
  • Format: Live, virtual classroom with interactive demos and Q&A.

Why Choose This Course?

  • Concise Yet Comprehensive Unlike multi-day programs, our course delivers the complete single-cell RNA-seq pipeline in just a few hours, helping you rapidly gain practical skills.
  • ‍Hands-On Focus The onsite version includes BYOD (Bring Your Own Data) so you can analyze your own datasets in real time, troubleshoot with experts, and leave with immediate results.
  • ‍Flexible & Interactive Opt for the online session if you need a concise overview. Prefer more depth and networking? Join our half-day onsite workshop for in-person mentorship.

What will we cover?

1. Single-Cell RNA-Seq Data Journey‍

  • Overview of scRNA-seq technologies
  • Significance of each step in the analysis workflow

2. Data Formats & Metadata

  • FASTQ, MTX, H5AD, and more
  • How to manage and interpret metadata

3. Quality Control & Normalization

  • Best practices for filtering and scaling data
  • Common pitfalls and troubleshooting tips

4. Dimensionality Reduction & Clustering

  • PCA, UMAP, t-SNE fundamentals
  • Biological relevance of clustering and subpopulation discovery

5. Data Integration & Batch Effect Correction

  • Approaches to merge datasets across conditions or experiments
  • Strategies for handling technical variations

6. Differential Gene Expression‍

  • Statistical testing, multiple-testing correction
  • Biological interpretation of gene expression changes

7. Cell Type Annotation & Reference Databases

  • Matching clusters to known cell populations
  • Leveraging public datasets for deeper insights

8. Advanced Exercises with Nygen & Other Tools‍

  • Brief overview of popular tools like Seurat and Scanpy and comparison with Nygen's capabilities
  • ‍LLM-augmented insights and real-time data visualization

9. BYOD Sessions (Onsite Only)‍

  • Analyze your own data under expert guidance
  • Immediate feedback and customized troubleshooting

Course Instructors

Parashar Dhapola PhD, Computational Genomics Co-founder at Nygen Analytics AB

Parashar Dhapola PhD, Computational Genomics

Co-founder & Lead Bioinformatician - Nygen Analytics

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Göran Karlsson PhD, Molecular Medine,

Co-founder and Head of Partnerships - Nygen Analytics

Learning Outcomes

By the end of this course, you will be able to:

  • 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

Registration Process

  1. Apply Online – Fill out the short registration form with details on your organisation or background. Let us know about your prefferd course format and time.
  2. Schedule Event - Once you request is received, our team will reach out to you. We will try our best to schedule the event at your preferred date and time.
  3. Secure Your Spot – Pay the course fee within the specified deadline.

Questions? Need more info about the application process, fees, or course details? Contact Us now. We look forward to helping you accelerate your single-cell research journey!

Register

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