End-to-end workflow
Work through QC, normalisation, integration, clustering, annotation, and differential expression as one coherent path, not isolated demos.
Accelerated Single-Cell Data Analysis
A hands-on course Nygen brings to your core facility, lab, or research group, online or on-site. Participants work the full single-cell workflow, from count matrices to interpretable biology, with expert guidance and time to troubleshoot their own data.
Why this course
Practical fluency in single-cell analysis, without a multi-day workshop.
Cell typing at the frontier
Learn why labels decide downstream biology, and how structured AI workflows support evidence-grounded annotation you can inspect and defend.
Built for facility delivery
Sized for small to mid-size groups so participants can work their own data. Help researchers complete early analysis steps themselves so facility experts can focus on harder review and biological questions.
Course agenda
Two parts across the day, with breaks and open Q&A.
Part 1 · Cell typing and AI annotation
Evidence-grounded labels you can defend
- 0:00-0:20 Intro and the single-cell data journey
- 0:20-0:50 Why annotation decides the biology
- 0:50-1:35 Using AI for cell-type annotation
- 1:35-2:15 From labels to biology you can act on
- 2:15-2:30 Break and open Q&A
Part 2 · Analysis workflow in practice
From matrices to shared, interpretable results
- 2:30-3:00 Bringing data into the session
- 3:00-3:30 Exploration, QC, and batch effects
- 3:30-4:05 Running AI annotation on your clusters
- 4:05-4:35 Cell selections and differential expression
- 4:35-4:50 Publishing and sharing results
- 4:50-5:00 Wrap-up and open Q&A
Course instructors
Learn from domain experts in single-cell biology and computational genomics.
Parashar Dhapola
PhD, Computational Genomics
PhD in computational genomics (Lund University). Single-cell computational biologist with deep methods expertise in annotation and analysis workflows. Co-founder and CEO at Nygen.
Goran Karlsson
Associate Professor, Lund University
PhD, Associate Professor in Molecular Hematology at Lund University. Leads a molecular hematology group and teaches the experimental and biological side of the course, from study design to reading results in context. Co-founder and Head of Partnerships at Nygen.
Practical details
How delivery, security, and booking work.
For facilities, labs, and groups only
We organise this course with core facilities, labs, and research groups. We do not take individual sign-ups. If you are an individual researcher, ask your facility or group lead to request a session for your wider team.
Explore our core facility locator mapHow the session runs
Hands-on work runs in a browser-based analysis environment provided for the course (ScarfWeb), including an evidence-grounded AI annotation workflow (CyteType). Sessions are sized for small to mid-size groups so participants can work on their own data. Participants need only a laptop and internet access. No local install, and no software purchase is required to take part.
Lunch on Nygen
When a session runs over the lunch hour, Nygen sponsors lunch for everyone. Participants stay in the room, keep the momentum, and use the break for informal Q&A.
Data security and support
Analysis runs on ISO 27001 and SOC 2 aligned cloud infrastructure. You can choose the data region, including EU options. Course data is not used beyond hosting and support for the session.
Open Trust CenterFrequently Asked Questions
No. We only run this course with core facilities, labs, and research groups. Ask your facility or group lead to request a session, and we will coordinate delivery for your wider team.
Yes. The course is completely free of charge. No purchase or license commitment is required from the facility or participants.
A laptop with internet access. The session uses a browser-based workbench; nothing to install locally.
Yes. The interactive portion supports participant datasets, and the breaks include open Q&A about your projects.
When a session runs over the lunch hour, Nygen sponsors lunch for everyone so participants can stay in the room and keep asking questions.
The core curriculum focuses on single-cell RNA-seq. Where audience interest allows, instructors can briefly cover CITE-seq and HTO upload.
Both. Choose the format that fits your calendar. For on-site sessions, the host provides a conference or lecture room sized for the audience.
Book this course for your facility or group
We only run this course with core facilities, labs, and research groups. We do not take individual sign-ups. Ask your facility or group lead to request a session, online or on-site. Free to host and attend.
Core facility spotlights and upcoming sessions
LMU Klinikum x Nygen - Accelerated Single Cell Data Analysis Course
Accelerated single-cell data analysis course with LMU Klinikum.
Read more →
i3S Porto x Nygen - Accelerated Single Cell Data Analysis Course
Hands-on single-cell RNA-Seq and multi-omics analysis course at i3S Porto.
Read more →
IGBMC x Nygen - Accelerated Single Cell Data Analysis Course
Accelerated single-cell data analysis course with IGBMC.
Read more →